RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17091
(1250 letters)
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 571 bits (1476), Expect = 0.0
Identities = 199/428 (46%), Positives = 282/428 (65%), Gaps = 10/428 (2%)
Query: 2 KPVLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGFE 61
KPV+ +VGRPNVGKSTLFNRLT RDA+VA+ PG+TRDR YGE + FI+IDTGG E
Sbjct: 1 KPVVAIVGRPNVGKSTLFNRLTGKRDAIVADTPGVTRDRIYGEAEWLGREFILIDTGGIE 60
Query: 62 PEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKS 121
P+ G ++ +Q + AI E+D+I+F+VDGR GL D+ I LRKS +P++LV+NK
Sbjct: 61 PD-DDGFEKQIREQAELAIEEADVILFVVDGRAGLTPADEEIAKILRKSNKPVILVVNKV 119
Query: 122 ENINSSISL-DFYELGIGNPHIISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIHSI 180
+ + +FY LG+G P+ ISA +G GI + L+ IL ELP ++ +++
Sbjct: 120 DGPDEEADAYEFYSLGLGEPYPISAEHGRGIGDLLDAILE-ELPEEEEEDEED------- 171
Query: 181 EYIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGI 240
E IK+AI+G+PNVGKS+LIN+LLGE RVI D GTTRDSI + FE + +KY LIDTAGI
Sbjct: 172 EPIKIAIIGRPNVGKSSLINALLGEERVIVSDIAGTTRDSIDTPFERDGQKYTLIDTAGI 231
Query: 241 RRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCV 300
RR+ K E +EK+SVI+TLK+I A+VV+L++DA + I+ QD+ IA E+GR+L++ V
Sbjct: 232 RRKGKVTEGVEKYSVIRTLKAIERADVVLLVIDATEGITEQDLRIAGLALEAGRALVIVV 291
Query: 301 NKWDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESINHVYDSSIIHLS 360
NKWD + + K ++++L FL +A FISA+ ++ +E+I+ Y+++ +S
Sbjct: 292 NKWDLVDEKTMEEFKKELRRRLPFLDYAPIVFISALTGQGVDKLLEAIDEAYENANRRIS 351
Query: 361 TSRITRALISAIKNHPPCRKKLIRPKLRYAHQGGKNPPIIVIHGNRLKYIGNDYKRYLEK 420
TS + R L A++ HPP K R K++YA Q G NPP V+ N + + YKRYLE
Sbjct: 352 TSVLNRVLEEAVERHPPPLVKGRRLKIKYATQVGTNPPTFVLFVNDPELLPFSYKRYLEN 411
Query: 421 YFYRTFSL 428
F
Sbjct: 412 QLREAFDF 419
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 563 bits (1453), Expect = 0.0
Identities = 199/427 (46%), Positives = 282/427 (66%), Gaps = 10/427 (2%)
Query: 4 VLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGFEPE 63
V+ +VGRPNVGKSTLFNRLT RDA+V++ PG+TRDR YG+ G + FI+IDTGG E +
Sbjct: 1 VVAIVGRPNVGKSTLFNRLTGKRDAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGIEED 60
Query: 64 VKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSEN 123
G+ ++ +Q + AI E+D+I+F+VDGR+GL +D+ I +LRKSG+P++LV NK +
Sbjct: 61 -DDGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDEEIAKWLRKSGKPVILVANKIDG 119
Query: 124 INS-SISLDFYELGIGNPHIISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIHSIEY 182
+++ +FY LG G P ISA +G GI + L+ IL + ++E
Sbjct: 120 KKEDAVAAEFYSLGFGEPIPISAEHGRGIGDLLDAIL-------ELLPEEEEEEEEEDGP 172
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRR 242
IK+AI+G+PNVGKSTL+N+LLGE RVI D GTTRDSI FE N KKY LIDTAGIRR
Sbjct: 173 IKIAIIGRPNVGKSTLVNALLGEERVIVSDIAGTTRDSIDIPFERNGKKYTLIDTAGIRR 232
Query: 243 RNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCVNK 302
+ K E +EK+SV++TLK+I A+VV+L+LDA + I+ QD+ IA E+G++L++ VNK
Sbjct: 233 KGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEGITEQDLRIAGLALEAGKALVIVVNK 292
Query: 303 WDSII-HNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESINHVYDSSIIHLST 361
WD + R+ K +++KL FL FA FISA+ ++ +++I+ VY+++ +ST
Sbjct: 293 WDLVKDEKTREEFKKELRRKLPFLDFAPIVFISALTGQGVDKLLDAIDEVYENANRRIST 352
Query: 362 SRITRALISAIKNHPPCRKKLIRPKLRYAHQGGKNPPIIVIHGNRLKYIGNDYKRYLEKY 421
S++ R L A+ HPP R K++YA Q G NPP V+ GNR + + YKRYLE
Sbjct: 353 SKLNRVLEEAVAAHPPPLVNGRRLKIKYATQVGTNPPTFVLFGNRPELLPFSYKRYLENQ 412
Query: 422 FYRTFSL 428
F F
Sbjct: 413 FREAFGF 419
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 493 bits (1271), Expect = e-163
Identities = 189/431 (43%), Positives = 273/431 (63%), Gaps = 9/431 (2%)
Query: 1 MKPVLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGF 60
PV+ +VGRPNVGKSTLFNRLT R A+V++ PG+TRDR YG+ + FI+IDTGG
Sbjct: 2 STPVVAIVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGREFILIDTGGL 61
Query: 61 EPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINK 120
+ + + + +Q AI E+D+I+F+VDGR+G+ D+ I LR+S +P++LV+NK
Sbjct: 62 DDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEIAKILRRSKKPVILVVNK 121
Query: 121 SENINSSISL-DFYELGIGNPHIISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIHS 179
+N+ + +FY LG G P ISA +G GI + L+ +L + +E
Sbjct: 122 IDNLKAEELAYEFYSLGFGEPVPISAEHGRGIGDLLDAVL------ELLPPDEEEEEEEE 175
Query: 180 IEYIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAG 239
+ IK+AI+G+PNVGKS+LIN++LGE RVI D GTTRDSI FE + +KY+LIDTAG
Sbjct: 176 TDPIKIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDSIDIEFERDGRKYVLIDTAG 235
Query: 240 IRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVC 299
IRR+ K E +EK+SV +TLK+I A+VV+L++DA + IS QD+ IA I E+GR +++
Sbjct: 236 IRRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQDLRIAGLIEEAGRGIVIV 295
Query: 300 VNKWDSIIHNQ--RKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESINHVYDSSII 357
VNKWD + ++ + K +++KL FL FA FISA+ ++ E+I +Y+ +
Sbjct: 296 VNKWDLVEEDEATMEEFKKKLRRKLPFLDFAPIVFISALTGQGLDKLFEAIKEIYECATR 355
Query: 358 HLSTSRITRALISAIKNHPPCRKKLIRPKLRYAHQGGKNPPIIVIHGNRLKYIGNDYKRY 417
+STS + R L A+ HPP + R K++YA Q NPP V+ GNR K + YKRY
Sbjct: 356 RISTSLLNRVLEDAVAKHPPPVRYGRRLKIKYATQVSTNPPTFVLFGNRPKALHFSYKRY 415
Query: 418 LEKYFYRTFSL 428
LE + F
Sbjct: 416 LENRLRKAFGF 426
>gnl|CDD|213530 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a
histidyl-tRNA synthetase in every completed genome.
Apparent second copies from Bacillus subtilis,
Synechocystis sp., and Aquifex aeolicus are slightly
shorter, more closely related to each other than to other
hisS proteins, and actually serve as regulatory subunits
for an enzyme of histidine biosynthesis. They were
excluded from the seed alignment and score much lower
than do single copy histidyl-tRNA synthetases of other
genomes not included in the seed alignment. These
putative second copies of HisS score below the trusted
cutoff. The regulatory protein kinase GCN2 of
Saccharomyces cerevisiae (YDR283c), and related proteins
from other species designated eIF-2 alpha kinase, have a
domain closely related to histidyl-tRNA synthetase that
may serve to detect and respond to uncharged tRNA(his),
an indicator of amino acid starvation; these regulatory
proteins are not orthologous and so score below the noise
cutoff [Protein synthesis, tRNA aminoacylation].
Length = 397
Score = 470 bits (1212), Expect = e-155
Identities = 170/354 (48%), Positives = 235/354 (66%), Gaps = 7/354 (1%)
Query: 867 SGEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMFRH 926
GEETDIV+KEMY+F D+ G +L+LRPEGTA V R+VIEN L+ P +L+Y GPMFR+
Sbjct: 51 VGEETDIVEKEMYTFKDK-GGRSLTLRPEGTAPVARAVIENKLLLPKPFKLYYIGPMFRY 109
Query: 927 ERPQYGRYRQFYQIGVEAIGFPGPDIDAELIIMCSRLWKNLNLKNICLELNSIGNFNERK 986
ERPQ GRYRQF+Q GVE IG P DAE+I + + + K L +K+ LE+NS+G R
Sbjct: 110 ERPQKGRYRQFHQFGVEVIGSDSPLADAEIIALAAEILKALGIKDFTLEINSLGILEGRL 169
Query: 987 KYCIDLINYIKKHKDSKWFCEDIKHSLYLNSLRVLDSKNLIIREILINAPKLLDYLEKDS 1046
+Y L+ Y+ KH D ED L N LR+LDSKN I+E+L APK+LD+L+++S
Sbjct: 170 EYREALLRYLDKHLDK--LGEDSVRRLEKNPLRILDSKNEKIQELLKEAPKILDFLDEES 227
Query: 1047 LDHFYGIQKILNYNNISYKINTKLVRGMDYYNRTVFEWTTDKLGSQNSICGGGRYDFLIK 1106
HF ++++L+ I Y I+ LVRG+DYY TVFE+ TD LG+Q SICGGGRYD L++
Sbjct: 228 RAHFEELKELLDALGIPYVIDPSLVRGLDYYTGTVFEFVTDGLGAQGSICGGGRYDGLVE 287
Query: 1107 KFSNKFVPASGFAIGIERLIELIKKININHNFSHQCDIYIVHVGKEAELKAFVLSENLRT 1166
+ PA GFAIGIERL+ L++++ + D+Y+V +G+EAEL+A L++ LR
Sbjct: 288 ELGGPPTPAVGFAIGIERLLLLLEELGLLPPEESSPDVYVVPLGEEAELEALKLAQKLRK 347
Query: 1167 LGLKVILNCVFNNIHESFKSQMKRANASNANFAAIIGENEIINNTLIIKDLRNK 1220
G++V ++ K Q+K A+ A FA IIGE+E+ N T+ +KDLR
Sbjct: 348 AGIRVEVDL----GGRKLKKQLKYADKLGARFAVIIGEDELANGTVTLKDLRTG 397
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 469 bits (1209), Expect = e-154
Identities = 167/374 (44%), Positives = 240/374 (64%), Gaps = 21/374 (5%)
Query: 867 SGEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMFRH 926
GEETDIV+KEMY+F D+ G +L+LRPEGTA V+R+VIE+ L P +L+Y GPMFR+
Sbjct: 55 VGEETDIVEKEMYTFQDK-GGRSLTLRPEGTAPVVRAVIEHKL---QPFKLYYIGPMFRY 110
Query: 927 ERPQYGRYRQFYQIGVEAIGFPGPDIDAELIIMCSRLWKNLNLKNICLELNSIGNFNERK 986
ERPQ GRYRQF+Q GVE IG P DAE+I + + + K L LK + L +NS+G+F R
Sbjct: 111 ERPQKGRYRQFHQFGVEVIGSDSPLADAEVIALAADILKALGLKGLKLLINSLGDFEIRA 170
Query: 987 KYCIDLINYIKKHKDSKWFCEDIKHSLYLNSLRVLDSKNLIIREILINAPKLLDYLEKDS 1046
Y L+ +++K D ED K L N LR+LD K+ +E+L +APKLLDYL+++S
Sbjct: 171 NYRKALVGFLEKGLDE--LDEDSKRRLETNPLRILDKKDKEDQELLKDAPKLLDYLDEES 228
Query: 1047 LDHFYGIQKILNYNNISYKINTKLVRGMDYYNRTVFEWTTDKLGSQNSICGGGRYDFLIK 1106
+HF ++++L+ I Y I+ +LVRG+DYY TVFE+ TD LG+Q ++CGGGRYD L++
Sbjct: 229 KEHFEELKELLDALGIPYVIDPRLVRGLDYYTGTVFEFVTDDLGAQGTVCGGGRYDGLVE 288
Query: 1107 KFSNKFVPASGFAIGIERLIELIKKININHNFSHQCDIYIVHVGKEAELKAFVLSENLRT 1166
+F PA GFAIG+ERL+ L++++ D+Y+V +G++AEL A L+E LR
Sbjct: 289 QFGGPPTPAVGFAIGVERLLLLLEELGEE-----PVDVYVVPLGEDAELAALKLAEKLRA 343
Query: 1167 LGLKVILNCVFNNIHESFKSQMKRANASNANFAAIIGENEIINNTLIIKDLRNKYEDPTL 1226
G++V L+ K Q K A+ S A F I+GE+E+ N T+ +KDLR
Sbjct: 344 AGIRVELDYGGRK----LKKQFKYADKSGARFVLILGEDELANGTVTVKDLRTG------ 393
Query: 1227 KQISISFKDAENYF 1240
+Q ++ +
Sbjct: 394 EQQTVPLDELVEAL 407
>gnl|CDD|223202 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 422 bits (1087), Expect = e-136
Identities = 164/381 (43%), Positives = 227/381 (59%), Gaps = 18/381 (4%)
Query: 867 SGEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMFRH 926
SGEETD+V+KEMY+F D+ G +L+LRPE TA V R+V EN L P +L+Y GP+FR+
Sbjct: 55 SGEETDVVEKEMYTFKDK-GGRSLALRPELTAPVARAVAENKLDLPKPLKLYYFGPVFRY 113
Query: 927 ERPQYGRYRQFYQIGVEAIGFPGPDIDAELIIMCSRLWKNLNLKNICLELNSIGNFNERK 986
ERPQ GRYRQFYQ GVE IG PD DAE+I + + + L + LE+NS G R
Sbjct: 114 ERPQKGRYRQFYQFGVEVIGSDSPDADAEVIALAVEILEALGIGGFTLEINSRGILEGRL 173
Query: 987 KYC-----IDLINYIKKHKDSKW--FCEDIKHSLYLNSLRVLDSKNLIIREILINAPKLL 1039
+Y L+ Y+ K ED K L N LRVLDSK +E+L NAP+LL
Sbjct: 174 EYLGIDQREALLRYLDKLDKIGKLELDEDSKRRLKTNPLRVLDSKKDSDQELLKNAPELL 233
Query: 1040 DYLEKDSLDHFYGIQKILNYNNISYKINTKLVRGMDYYNRTVFEWTTDKLGSQNSICGGG 1099
DYL+++SL+H + +L+ ISY+I+ LVRG+DYY TVFE TD LG+Q S+CGGG
Sbjct: 234 DYLDEESLEHLEELLALLDALGISYEIDPSLVRGLDYYTGTVFEAVTDGLGAQGSVCGGG 293
Query: 1100 RYDFLIKKFSNKFVPASGFAIGIERLIELIKKININHNFSHQCDIYIVHVGKEAELKAFV 1159
RYD L+++F K PA GFAIG+ERLI +++ + D+Y+V +G++AE +A
Sbjct: 294 RYDGLVEEFGGKPTPAVGFAIGVERLILALEEEGKEDPVETRVDVYVVPLGEDAEPEALK 353
Query: 1160 LSENLRTLGLKVILNCVFNNIHESFKSQMKRANASNANFAAIIGENEIINNTLIIKDLRN 1219
L++ LR G+ V ++ K Q K A+ A FA I+GE+E+ N + +KDL
Sbjct: 354 LAQKLRAAGISVEVDY----SGRKLKKQFKYADKLGARFAVILGEDELANGVVTVKDLAT 409
Query: 1220 KYEDPTLKQISISFKDAENYF 1240
+Q + +
Sbjct: 410 G------EQEEVPLDELVEEL 424
>gnl|CDD|183031 PRK11194, PRK11194, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 372
Score = 411 bits (1059), Expect = e-133
Identities = 171/347 (49%), Positives = 231/347 (66%), Gaps = 13/347 (3%)
Query: 535 ELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQISFDGTR 594
ELGE PFRA Q+ KWI+ +G DF++MT+++ LR+KLK I+AP + +Q S DGT
Sbjct: 22 ELGEKPFRADQVMKWIYHYGCDDFDEMTNINKVLREKLKEVAEIRAPEVAEEQRSSDGTI 81
Query: 595 KWIFHVKKNIIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVGEIIGQLW 654
KW V +ETV+IPE +R TLC+S+QVGCA+ C FCST +QGF RNL V EIIGQ+W
Sbjct: 82 KWAIAVGDQRVETVYIPEDDRATLCVSSQVGCALECKFCSTAQQGFNRNLRVSEIIGQVW 141
Query: 655 VTEFKLRREKNIKI-NSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYGLSRRH 713
R K I G+R ITN+VMMGMGEPLLN + + A++++L D +GLS+R
Sbjct: 142 ------RAAKIIGAAKVTGQRPITNVVMMGMGEPLLNLNNVVPAMEIMLDDFGFGLSKRR 195
Query: 714 VILSTSGIIPMIDKLAQECPVELAVSLHASNNNLRNKLVPISKKYPLKELILACHRYITY 773
V LSTSG++P +DKL V LA+SLHA N+ LR+++VPI+KKY ++ + A RY+
Sbjct: 196 VTLSTSGVVPALDKLGDMIDVALAISLHAPNDELRDEIVPINKKYNIETFLAAVRRYLEK 255
Query: 774 SP--RHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFNCFPNSNLICSK 831
S + +T EY ML +ND HA +L L++ T CKINLIP+N FP + S
Sbjct: 256 SNANQGRVTVEYVMLDHVNDGTEHAHQLAELLKD----TPCKINLIPWNPFPGAPYGRSS 311
Query: 832 NSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQLSGEETDIVKKEM 878
NSRI F+K+LM G V +RK RG+DI+AACGQL+G+ D K+ +
Sbjct: 312 NSRIDRFSKVLMEYGFTVIVRKTRGDDIDAACGQLAGDVIDRTKRTL 358
>gnl|CDD|223890 COG0820, COG0820, Predicted Fe-S-cluster redox enzyme [General
function prediction only].
Length = 349
Score = 392 bits (1010), Expect = e-126
Identities = 169/345 (48%), Positives = 228/345 (66%), Gaps = 16/345 (4%)
Query: 535 ELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQISFDGTR 594
ELG FRAKQL KWI++ GV DF++MTDLS LR KLK + +I ++ Q S DGT
Sbjct: 18 ELGLKKFRAKQLFKWIYQKGVDDFDEMTDLSKGLRAKLKEAFFINLLKVVEVQESSDGTI 77
Query: 595 KWIFHVKKN--IIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVGEIIGQ 652
KW+F V + +IETV IPEK+RNTLC+S+QVGC + C FC+TG+ G RNL+ GEI+ Q
Sbjct: 78 KWLFEVLPDGTMIETVLIPEKDRNTLCVSSQVGCPVGCTFCATGQGGLNRNLSAGEIVEQ 137
Query: 653 LWVTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYGLSRR 712
+ + L + R+I+N+V MGMGEPLLN + + AL++I D GLS+R
Sbjct: 138 VLLAAKALGEDF--------GRRISNVVFMGMGEPLLNLDNVVKALEIINDDEGLGLSKR 189
Query: 713 HVILSTSGIIPMIDKLAQE-CPVELAVSLHASNNNLRNKLVPISKKYPLKELILACHRYI 771
+ +STSGI+P I KLA E V LA+SLHA N+ LR++L+PI+KKYP++EL+ A Y
Sbjct: 190 RITVSTSGIVPRIRKLADEQLGVALAISLHAPNDELRDQLMPINKKYPIEELLEAIRYYP 249
Query: 772 TYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFNCFPNSNLICSK 831
S R +TFEY +L G+ND+ HA EL L++ CK+NLIP+N P S+ S
Sbjct: 250 EKSGRR-VTFEYVLLDGVNDSLEHAKELAKLLKGIP----CKVNLIPYNPVPGSDYERSS 304
Query: 832 NSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQLSGEETDIVKK 876
RI+ F KIL +G+ VT+RK RG+DI+AACGQL G+ +K
Sbjct: 305 KERIRKFLKILKKAGVLVTVRKTRGDDIDAACGQLRGKRIKRTRK 349
>gnl|CDD|232798 TIGR00048, TIGR00048, 23S rRNA m2A2503 methyltransferase. A
Staphylococcus sciuri plasmid-borne member of this
family, Cfr, has been identified as essential to
transferrable resistance to chloramphenicol and
florfenicol by an unknown mechanism. A 14-15 residue
cluster with four perfectly conserved Cys residues
suggests this protein may be an enzyme with an
iron-sulfur cluster. The Cys cluster is part of the
radical SAM domain, suggested to provide a general
mechanism by which the Fe-S center cleaves
S-adenosylmethionine to initiate radical-based
catalysis. Members of this family lack apparent
transmembrane domains [Protein synthesis, tRNA and rRNA
base modification].
Length = 355
Score = 356 bits (916), Expect = e-113
Identities = 156/339 (46%), Positives = 222/339 (65%), Gaps = 16/339 (4%)
Query: 530 KNIVHELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQIS 589
+ + +LGE PFRAKQ+ KW++ G F+ MT+LS LR+KL I+ P I +Q S
Sbjct: 18 RQWLKDLGEKPFRAKQIMKWLYHKGCDSFDDMTNLSKVLREKLNEVFEIRTPEIAHEQRS 77
Query: 590 FDGTRKWIFHVKKN-IIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVGE 648
DGT K++F + IETV IPE +R T+C+S+QVGCA+ C FC+T + GF RNL E
Sbjct: 78 SDGTIKYLFALGDGQTIETVLIPEDDRATVCVSSQVGCALGCTFCATAKGGFNRNLEASE 137
Query: 649 IIGQLWVTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYG 708
IIGQ+ + KI + +++N+V MGMGEPLLN + A++++ D +G
Sbjct: 138 IIGQVLRVQ---------KIVGETGERVSNVVFMGMGEPLLNLNEVVKAMEIMNDDFGFG 188
Query: 709 LSRRHVILSTSGIIPMIDKLA-QECPVELAVSLHASNNNLRNKLVPISKKYPLKELILAC 767
+S+R + +STSG++P IDKLA + V LA+SLHA N+ +R+ L+PI+KKY ++ L+ A
Sbjct: 189 ISKRRITISTSGVVPKIDKLADKMLQVALAISLHAPNDEIRSSLMPINKKYNIETLLAAV 248
Query: 768 HRYITYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFNCFPNSNL 827
RY+ + R +TFEY +L G+ND HA EL L++ T CK+NLIP+N FP ++
Sbjct: 249 RRYLEKTGRR-VTFEYVLLDGVNDQVEHAEELAELLKG----TKCKVNLIPWNPFPEADY 303
Query: 828 ICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQL 866
NS+I FAK+LM+ G VTIRK RG+DI+AACGQL
Sbjct: 304 GRPSNSQIDRFAKVLMSYGFTVTIRKSRGDDIDAACGQL 342
>gnl|CDD|184686 PRK14454, PRK14454, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 342
Score = 310 bits (796), Expect = 5e-96
Identities = 150/340 (44%), Positives = 216/340 (63%), Gaps = 20/340 (5%)
Query: 530 KNIVHELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQIS 589
K + E GE FRAKQ+ WI+K GV+DF++MT++ +LR+KLK + YI P I+ +S
Sbjct: 13 KEWMKENGEKKFRAKQIFDWIYKKGVTDFDEMTNIPKNLREKLKENFYIGIPKIVKKLVS 72
Query: 590 -FDGTRKWIFHVK-KNIIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVG 647
DGT K++F ++ NIIE+V + K+ N++C+STQVGC + C FC++ G VRNLT G
Sbjct: 73 KIDGTVKFLFELEDGNIIESVVMKYKHGNSICVSTQVGCRMGCKFCASTIGGMVRNLTAG 132
Query: 648 EIIGQLWVTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAY 707
E++ Q+ + N G+R I+NIV+MG GEPL NY++ + LK++ S +
Sbjct: 133 EMLDQILAAQ-----------NDIGER-ISNIVLMGSGEPLDNYENVMKFLKIVNSPYGL 180
Query: 708 GLSRRHVILSTSGIIPMIDKLA-QECPVELAVSLHASNNNLRNKLVPISKKYPLKELILA 766
+ +RH+ LST GI+P I +LA + + LA+SLHA N+ LR K++PI+ KY ++ELI A
Sbjct: 181 NIGQRHITLSTCGIVPKIYELADENLQITLAISLHAPNDELRKKMMPIANKYSIEELIEA 240
Query: 767 CHRYITYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFNCFPNSN 826
C YI + R ITFEY ++ G+ND+ A EL L+ K + C +NLIP N +
Sbjct: 241 CKYYINKTNRR-ITFEYALVKGVNDSKEDAKELGKLL-KGML---CHVNLIPVNEVKENG 295
Query: 827 LICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQL 866
S +IK F IL +GI TIR+ G+DINAACGQL
Sbjct: 296 FKKSSKEKIKKFKNILKKNGIETTIRREMGSDINAACGQL 335
>gnl|CDD|164576 CHL00201, syh, histidine-tRNA synthetase; Provisional.
Length = 430
Score = 307 bits (789), Expect = 9e-94
Identities = 164/382 (42%), Positives = 229/382 (59%), Gaps = 15/382 (3%)
Query: 868 GEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGP-KRLWYSGPMFRH 926
GE TDIV KEMY F D N D ++LRPEGTA ++R+ IEN + Y +RLWYSGPMFR+
Sbjct: 56 GETTDIVNKEMYRFTDRSNRD-ITLRPEGTAGIVRAFIENKMDYHSNLQRLWYSGPMFRY 114
Query: 927 ERPQYGRYRQFYQIGVEAIGFPGPDIDAELIIMCSRLWKNLNLKNICLELNSIGNFNERK 986
ERPQ GR RQF+Q+G+E IG D E+I + +++ L +KN+ L++NSIG +R+
Sbjct: 115 ERPQSGRQRQFHQLGIEFIGSIDARADTEVIHLAMQIFNELQVKNLILDINSIGKLEDRQ 174
Query: 987 KYCIDLINYIKKHKDSKWFCEDIKHSLYLNSLRVLDSKNLIIREILINAPKLLDYLEKDS 1046
Y + L+ Y+ +++D D ++ LY N +R+LDSKNL +EIL APK+ D+L +S
Sbjct: 175 SYQLKLVEYLSQYQDD--LDTDSQNRLYSNPIRILDSKNLKTQEILDGAPKISDFLSLES 232
Query: 1047 LDHFYGIQKILNYNNISYKINTKLVRGMDYYNRTVFEWTTDKLGSQNSICGGGRYDFLIK 1106
+HFY + LN NI YKIN KLVRG+DYYN T FE T Q++ICGGGRYD LI
Sbjct: 233 TEHFYDVCTYLNLLNIPYKINYKLVRGLDYYNDTAFEIKTLSSNGQDTICGGGRYDSLIH 292
Query: 1107 KFSNKFVPASGFAIGIERLIELIK-KININHNFSHQCDIYIVHVGKEAELKAFVLSENLR 1165
+ PA G AIG+ERL+ + K I + D+YI G +A+ K + + + L
Sbjct: 293 QLGGPKTPAVGCAIGLERLLLIAKDNIILPK---QSIDVYIATQGLKAQKKGWEIIQFLE 349
Query: 1166 TLGLKVILNCVFNNIHESFKSQMKRANASNANFAAIIGENEIINNTLIIKDLRNKYEDPT 1225
+K L+ +N H+ Q+K+A A I+G+NEI++N + IK L E
Sbjct: 350 KQNIKFELDLSSSNFHK----QIKQAGKKRAKACIILGDNEIMDNCITIKWL---DEQVQ 402
Query: 1226 LKQISISFKDAENYFYKKIIKN 1247
+FK +Y KKI N
Sbjct: 403 ENAQYSNFKQEISYLKKKIAFN 424
>gnl|CDD|237720 PRK14463, PRK14463, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 349
Score = 299 bits (766), Expect = 1e-91
Identities = 130/334 (38%), Positives = 198/334 (59%), Gaps = 20/334 (5%)
Query: 536 LGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQISFDGTRK 595
G+ FRAKQ+ KW+++ F +MT+LS LR +L+ + I + ++S DGTRK
Sbjct: 22 QGKERFRAKQIFKWLYQRDARSFAEMTNLSKDLRAELEETARISNLEPEAVEVSRDGTRK 81
Query: 596 WIFHVKK-NIIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVGEIIGQLW 654
++F ++ N +E+V IP+++RNTLCIS+QVGCA+ C FC TG RNLT EI+ Q+
Sbjct: 82 YLFRLEDGNAVESVLIPDEDRNTLCISSQVGCAMGCAFCLTGTFRLTRNLTTAEIVNQV- 140
Query: 655 VTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYGLSRRHV 714
++R+ ++ NIV MGMGEPL N + I AL+++ S R V
Sbjct: 141 ---CAVKRDVPVR----------NIVFMGMGEPLANLDNVIPALQILTDPDGLQFSTRKV 187
Query: 715 ILSTSGIIPMIDKLAQECPVELAVSLHASNNNLRNKLVPISKKYPLKELILACHRYITYS 774
+STSG++P +++L +E V LAVSL+A+ + +R++++P++++YPL EL+ AC +
Sbjct: 188 TVSTSGLVPEMEELGREVTVNLAVSLNATTDEVRDRIMPVNRRYPLAELLAACKAFPLPG 247
Query: 775 PRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFNCFPNSNLICSKNSR 834
R IT EY M+ G+ND+ A L+ L+ K+NLIPFN +
Sbjct: 248 -RRKITIEYVMIRGLNDSLEDAKRLVRLLSD----IPSKVNLIPFNEHEGCDFRSPTQEA 302
Query: 835 IKIFAKILMNSGIFVTIRKIRGNDINAACGQLSG 868
I F K L++ + V R RG+DI+AACGQL G
Sbjct: 303 IDRFHKYLLDKHVTVITRSSRGSDISAACGQLKG 336
>gnl|CDD|172935 PRK14460, PRK14460, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 354
Score = 296 bits (760), Expect = 9e-91
Identities = 139/342 (40%), Positives = 194/342 (56%), Gaps = 13/342 (3%)
Query: 532 IVHELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQISFD 591
I ELGE FRA+Q+ +W+ + G DF+ MT++S +LR +L I P + + Q S D
Sbjct: 16 ITAELGEPRFRARQIWQWLWQKGARDFDSMTNVSKALRARLAEKAVINWPEVETVQTSSD 75
Query: 592 GTRKWIFHVKKN-IIETVFIPEKNRN-TLCISTQVGCAINCIFCSTGRQGFVRNLTVGEI 649
GT K++ + ++ETV IP K+R T C+S QVGCA+ C FCSTG GF RN+T+GEI
Sbjct: 76 GTVKFLLRLADGALVETVLIPSKSRRYTQCLSCQVGCAMGCTFCSTGTMGFERNMTMGEI 135
Query: 650 IGQLWVTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYGL 709
+GQ+ V L N + N+V MGMGEPLLN + +L+ + ++
Sbjct: 136 LGQVLVAREHLGD------NGPDHPILRNLVFMGMGEPLLNLDEVMRSLRTLNNEKGLNF 189
Query: 710 SRRHVILSTSGIIPMIDKLAQECPVELAVSLHASNNNLRNKLVPISKKYPLKELILACHR 769
S R + +ST GI + +L + LAVSLHA N LR +++P + ++PL +LI A
Sbjct: 190 SPRRITVSTCGIEKGLRELGESGLAFLAVSLHAPNQELRERIMPKAARWPLDDLIAALKS 249
Query: 770 YITYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFNCFPNSNLIC 829
Y R +TFEY +L G+ND+ HA EL+ L+ + K CK+NLI +N
Sbjct: 250 Y-PLKTRERVTFEYLLLGGVNDSLEHARELVRLLSRTK----CKLNLIVYNPAEGLPYSA 304
Query: 830 SKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQLSGEET 871
RI F K L + GI IRK +G DI AACGQL EE
Sbjct: 305 PTEERILAFEKYLWSKGITAIIRKSKGQDIKAACGQLKAEEL 346
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 299 bits (768), Expect = 1e-87
Identities = 140/432 (32%), Positives = 236/432 (54%), Gaps = 23/432 (5%)
Query: 4 VLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGFEPE 63
V+ +VGRPNVGKSTL NR+ R+A+V + PG+TRDR + F ++DTGG+E +
Sbjct: 277 VVAIVGRPNVGKSTLVNRILGRREAVVEDTPGVTRDRVSYDAEWAGTDFKLVDTGGWEAD 336
Query: 64 VKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSEN 123
V+ GI + Q + A+ +D ++F+VDG+ GL D+ I LR++G+P+VL +NK ++
Sbjct: 337 VE-GIDSAIASQAQIAVSLADAVVFVVDGQVGLTSTDERIVRMLRRAGKPVVLAVNKIDD 395
Query: 124 INS-SISLDFYELGIGNPHIISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIHSIEY 182
S + +F++LG+G P+ ISA++G G+ + L+ L K +K +
Sbjct: 396 QASEYDAAEFWKLGLGEPYPISAMHGRGVGDLLDEALDS---LKV--AEKTSGFLTPSGL 450
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRR 242
+VA+VG+PNVGKS+L+N L E R + D GTTRD + + E + + ++ IDTAGI+R
Sbjct: 451 RRVALVGRPNVGKSSLLNQLTHEERAVVNDLAGTTRDPVDEIVEIDGEDWLFIDTAGIKR 510
Query: 243 RNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCVNK 302
R E +S ++T +I + + + L DA Q IS QD+ + + ++GR+L++ NK
Sbjct: 511 RQHKLTGAEYYSSLRTQAAIERSELALFLFDASQPISEQDLKVMSMAVDAGRALVLVFNK 570
Query: 303 WDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESINHVYDSSIIHLSTS 362
WD + +R+ ++ K + + +++A +SA + N ++ +S + T
Sbjct: 571 WDLMDEFRRQRLERLWKTEFDRVTWARRVNLSAKTGWHTNRLAPAMQEALESWDQRIPTG 630
Query: 363 RITRALISAIKNHPPCRKKLIRPKLRYAHQGGKNPPIIVI-------HGNRLKYIGNDYK 415
++ L HP + +P++ +A Q PP VI HG Y+
Sbjct: 631 KLNAFLGKIQAEHPHPLRGGKQPRILFATQASTRPPRFVIFTTGFLEHG---------YR 681
Query: 416 RYLEKYFYRTFS 427
R+LE+ F
Sbjct: 682 RFLERSLREEFG 693
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 286 bits (735), Expect = 1e-85
Identities = 151/436 (34%), Positives = 244/436 (55%), Gaps = 31/436 (7%)
Query: 2 KPVLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDR-HYGEGYIGKKSFIIIDTGGF 60
PV+ +VGRPNVGKSTL NR+ R+A+V + PG+TRDR Y + G++ F ++DTGG+
Sbjct: 38 LPVVAVVGRPNVGKSTLVNRILGRREAVVEDVPGVTRDRVSYDAEWNGRR-FTVVDTGGW 96
Query: 61 EPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINK 120
EP+ K G+ + +Q + A+ +D ++F+VD G D+ + LR+SG+P++L NK
Sbjct: 97 EPDAK-GLQASVAEQAEVAMRTADAVLFVVDATVGATATDEAVARVLRRSGKPVILAANK 155
Query: 121 --SENINSSISLDFYELGIGNPHIISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIH 178
E + + + LG+G PH +SAL+G G+ + L+ +L LP E +
Sbjct: 156 VDDERGEADAA-ALWSLGLGEPHPVSALHGRGVGDLLDAVLAA-LP--------EVPRVG 205
Query: 179 SIEY--IKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILID 236
S +VA+VGKPNVGKS+L+N L GE R + D GTT D + SL E K + +D
Sbjct: 206 SASGGPRRVALVGKPNVGKSSLLNKLAGEERSVVDDVAGTTVDPVDSLIELGGKTWRFVD 265
Query: 237 TAGIRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSL 296
TAG+RRR K E ++ ++T +I A V ++L+DA + IS QD + + + E+GR+L
Sbjct: 266 TAGLRRRVKQASGHEYYASLRTHAAIEAAEVAVVLIDASEPISEQDQRVLSMVIEAGRAL 325
Query: 297 IVCVNKWDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESINHVYDSSI 356
++ NKWD + ++R ++ I ++L + +A ISA ++ + ++ +S
Sbjct: 326 VLAFNKWDLVDEDRRYYLEREIDRELAQVPWAPRVNISAKTGRAVDKLVPALETALESWD 385
Query: 357 IHLSTSRIT---RALISAIKNHPPCRK-KLIRPKLRYAHQGGKNPPIIVIH--GNRLKYI 410
+ T R+ L++A PP R K P++ +A Q PP V+ G ++
Sbjct: 386 TRIPTGRLNAWLGELVAA--TPPPVRGGKQ--PRILFATQASTRPPTFVLFTTG----FL 437
Query: 411 GNDYKRYLEKYFYRTF 426
Y+R+LE+ TF
Sbjct: 438 EAGYRRFLERRLRETF 453
>gnl|CDD|184689 PRK14459, PRK14459, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 373
Score = 278 bits (714), Expect = 5e-84
Identities = 130/360 (36%), Positives = 198/360 (55%), Gaps = 23/360 (6%)
Query: 522 ADFAESIDKNIVHELGEMPFRAKQLQKWIHKFG--VSDFNKMTDLSMSLRKKLKNSVYIK 579
AD + + V ELG FRAKQL + H FG +D +MTDL + R++L +++
Sbjct: 25 ADLTPAERREAVAELGLPAFRAKQLAR--HYFGRLTADPAQMTDLPAAAREELAEALF-- 80
Query: 580 APHIMSD--QISFDG--TRK--WIFHVKKNIIETVFIPEKNRNTLCISTQVGCAINCIFC 633
P +++ + D TRK W H ++E+V + +R TLCIS+Q GC + C FC
Sbjct: 81 -PTLLTPVRTLEADDGTTRKTLWRLH-DGTLVESVLMRYPDRATLCISSQAGCGMACPFC 138
Query: 634 STGRQGFVRNLTVGEIIGQLWVTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKS 693
+TG+ G RNL+ EI+ Q+ LR + G +++N+V MGMGEPL NYK
Sbjct: 139 ATGQGGLTRNLSTAEIVEQVRAAARALRDGE----VPGGPGRLSNVVFMGMGEPLANYKR 194
Query: 694 TIGALKLILSD--HAYGLSRRHVILSTSGIIPMIDKLAQE-CPVELAVSLHASNNNLRNK 750
+ A++ I + G+S R+V +ST G++P I KLA E PV LAVSLHA ++ LR++
Sbjct: 195 VVAAVRRITAPAPEGLGISARNVTVSTVGLVPAIRKLADEGLPVTLAVSLHAPDDELRDE 254
Query: 751 LVPISKKYPLKELILACHRYITYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILT 810
LVP++ ++ + E++ A Y + R ++ EY ++ IND A L + +
Sbjct: 255 LVPVNTRWKVDEVLDAARYYADATGRR-VSIEYALIRDINDQPWRADLLGKKLHG-RGGG 312
Query: 811 SCKINLIPFNCFPNSNLICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQLSGEE 870
+NLIP N P S S + F + L +G+ T+R RG +I+ ACGQL+ EE
Sbjct: 313 WVHVNLIPLNPTPGSKWTASPPEVEREFVRRLRAAGVPCTVRDTRGQEIDGACGQLAAEE 372
>gnl|CDD|184693 PRK14467, PRK14467, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 348
Score = 273 bits (701), Expect = 1e-82
Identities = 138/354 (38%), Positives = 203/354 (57%), Gaps = 25/354 (7%)
Query: 530 KNIVHELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQIS 589
+ V ELG +RAKQ+ KW++K V+DF++MTDLS R+ LK + + D++
Sbjct: 13 EEFVVELGWEKYRAKQIAKWVYKKKVTDFDEMTDLSKEDRQLLKENFEFHTLE-LLDRVE 71
Query: 590 FDGTRKWIFHVKK-NIIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVGE 648
D + K++F K + IETV I E++ TLC+S+QVGCA+ C FC+T + G +RNL E
Sbjct: 72 ADDSVKYLFKTKDGHTIETVLIKERDHLTLCVSSQVGCAVGCKFCATAKDGLIRNLRTAE 131
Query: 649 IIGQLWVTEFKLRREKNIKINSQ---GKRQITNIVMMGMGEPLLNYKSTIGALKLILSDH 705
II Q I Q G+ +I N+V MGMGEPL NY++ A++++ S
Sbjct: 132 IIDQY--------------IQVQKFLGENRIRNVVFMGMGEPLANYENVRKAVQIMTSPW 177
Query: 706 AYGLSRRHVILSTSGIIPMIDKLAQEC---PVELAVSLHASNNNLRNKLVPISKKYPLKE 762
LS+R + +STSGII I ++A++ V LAVSL+AS+ LR +++PISK L+E
Sbjct: 178 GLDLSKRRITISTSGIIHQIKRMAEDPVMPEVNLAVSLNASSQKLRERIMPISKTNTLEE 237
Query: 763 LILACHRYITYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFNCF 822
L+ +Y P I EY ++ G+ND+ A+ L L+ KNK K+NLIPFN
Sbjct: 238 LMEVLKQY-PLPPGRRIMLEYVLIKGVNDSPEDALRLAQLIGKNK--KKFKVNLIPFNPD 294
Query: 823 PNSNLICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQLSGEETDIVKK 876
P + R+ F KIL ++GI +R +G DI ACGQL + ++K
Sbjct: 295 PELPYERPELERVYKFQKILWDNGISTFVRWSKGVDIFGACGQLRKKRVQLLKV 348
>gnl|CDD|184688 PRK14457, PRK14457, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 345
Score = 271 bits (694), Expect = 1e-81
Identities = 119/346 (34%), Positives = 188/346 (54%), Gaps = 28/346 (8%)
Query: 530 KNIVHELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVY-IKAPHIMSDQI 588
++ G+ FR +QL W++ GV ++++ L + R+ LK+ I I+ +
Sbjct: 13 EDWAVAQGQPAFRGRQLHDWLYNKGVRSLDEISVLPKAWRESLKDDGVPIGRLTIVERSV 72
Query: 589 SFDGTRKWIFHVKKN-IIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVG 647
+ DGT K + + IIETV IP + R T+C+S+QVGC + C FC+TG+ G R+L
Sbjct: 73 APDGTLKLLLSTEDGEIIETVGIPTEKRLTVCVSSQVGCPMACDFCATGKGGLKRSLKAH 132
Query: 648 EIIGQLWVTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAY 707
EI+ Q+ + + +R+++++V MGMGEPLLN + A++ + D
Sbjct: 133 EIVDQV------------LTVQEDMQRRVSHVVFMGMGEPLLNIDEVLAAIRCLNQD--L 178
Query: 708 GLSRRHVILSTSGIIPMIDKLAQ-------ECPVELAVSLHASNNNLRNKLVPISKKYPL 760
G+ +R + +ST G+ I +LA+ LAVSLHA N LR L+P +K YP+
Sbjct: 179 GIGQRRITVSTVGVPKTIPQLAELAFQRLGRLQFTLAVSLHAPNQKLRETLIPSAKNYPI 238
Query: 761 KELILACHRYITYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFN 820
+ L+ C Y+ + R ++FEY +L G+ND HA EL +L+R + +NLIP+N
Sbjct: 239 ENLLEDCRHYVAITGRR-VSFEYILLGGVNDLPEHAEELANLLRGFQ----SHVNLIPYN 293
Query: 821 CFPNSNLICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQL 866
RI+ F ++L G+ V++R RG D NAACGQL
Sbjct: 294 PIDEVEFQRPSPKRIQAFQRVLEQRGVAVSVRASRGLDANAACGQL 339
>gnl|CDD|237718 PRK14461, PRK14461, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 371
Score = 267 bits (683), Expect = 6e-80
Identities = 124/344 (36%), Positives = 196/344 (56%), Gaps = 8/344 (2%)
Query: 535 ELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQISFDG-T 593
G+ FRA+QL + ++ MTDL ++LR++L + + + QI +G T
Sbjct: 24 AWGQPAFRARQLYRHLYVNLADSVLAMTDLPLALRERLTAELPLSTLRLEQVQIGDNGLT 83
Query: 594 RKWIFHVKKN-IIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVGEIIGQ 652
RK +F + ++ETV + +R T+C+STQ GC + C+FC+TG G +RNL+ GEI+ Q
Sbjct: 84 RKALFRLPDGAVVETVLMIYPDRATVCVSTQAGCGMGCVFCATGTLGLLRNLSSGEIVAQ 143
Query: 653 LWVTEFKLRRE--KNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYGLS 710
+ +LR K ++ ++TN+V MGMGEP NY A++ + + L
Sbjct: 144 VIWASRELRAMGAAISKRHAGPVGRVTNLVFMGMGEPFANYDRWWQAVERLHDPQGFNLG 203
Query: 711 RRHVILSTSGIIPMIDKLAQE-CPVELAVSLHASNNNLRNKLVPISKKYPLKELILACHR 769
R + +ST G++ I +LA E P+ LA+SLHA ++ LR++L+P++++YP+ +L+ A
Sbjct: 204 ARSMTVSTVGLVKGIRRLANERLPINLAISLHAPDDALRSELMPVNRRYPIADLMAATRD 263
Query: 770 YITYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTS--CKINLIPFNCFPNSNL 827
YI + R ++FEY +L G ND A L L+R +NLIP+N P + L
Sbjct: 264 YIAKTRRR-VSFEYVLLQGKNDHPEQAAALARLLRGEAPPGPLLVHVNLIPWNPVPGTPL 322
Query: 828 ICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQLSGEET 871
S+ R+ F +IL + GI T+R RG +I AACGQL+G T
Sbjct: 323 GRSERERVTTFQRILTDYGIPCTVRVERGVEIAAACGQLAGRHT 366
>gnl|CDD|172944 PRK14469, PRK14469, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 343
Score = 263 bits (675), Expect = 3e-79
Identities = 135/339 (39%), Positives = 199/339 (58%), Gaps = 21/339 (6%)
Query: 531 NIVHELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQIS- 589
+ + ELG +RA Q+ WI+K V +F++MT+LS R L I P ++ Q+S
Sbjct: 14 SEITELGLEKYRADQILDWIYKKKVFNFDEMTNLSKDHRALLSEHFSIPFPKLLDKQVSK 73
Query: 590 FDGTRKWIFHVK-KNIIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVGE 648
DGT K+++ ++ N IE+V + +R T CISTQVGC + CIFC+TG+ GFVRNLT GE
Sbjct: 74 IDGTTKFLWELEDGNTIESVMLFHPDRITACISTQVGCPVKCIFCATGQSGFVRNLTTGE 133
Query: 649 IIGQLWVTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYG 708
I+ Q+ L EK K + N+V MGMGEPLLNY++ I ++K++
Sbjct: 134 IVSQI------LAMEKEEKKK------VGNVVYMGMGEPLLNYENVIKSIKILNHKKMKN 181
Query: 709 LSRRHVILSTSGIIPMIDKLAQECP-VELAVSLHASNNNLRNKLVPISKKYPLKELILAC 767
+ R + +ST GI I +LA+E V+LA+SLHA N R+++VP++KKY ++E+I A
Sbjct: 182 IGIRRITISTVGIPEKIIQLAEEGLDVKLALSLHAPTNFKRDQIVPLNKKYSIEEIINAV 241
Query: 768 HRYITYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFNCFPNSNL 827
Y + +T EY ++ G ND A +L L++ K+ +NLIP N L
Sbjct: 242 KIYQKKTGNR-VTIEYILIKGFNDEIEDAKKLAELLKGLKVF----VNLIPVNPTV-PGL 295
Query: 828 ICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQL 866
RI+ F +IL+ +GI IR+ +G+DI AACGQL
Sbjct: 296 EKPSRERIERFKEILLKNGIEAEIRREKGSDIEAACGQL 334
>gnl|CDD|184694 PRK14468, PRK14468, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 343
Score = 263 bits (675), Expect = 4e-79
Identities = 122/332 (36%), Positives = 181/332 (54%), Gaps = 20/332 (6%)
Query: 540 PFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQISFDGTRKWIFH 599
+R QL +W++ G F+ MT+L +LR +L + + S DG+ K++F
Sbjct: 16 GYRRAQLAEWLYAQGARTFDAMTNLPKALRAELAREYRLSPFREVETFRSQDGSVKYLFT 75
Query: 600 V---KKNIIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVGEIIGQLWVT 656
+ K+ E V++P +R T+C+ST VGC C FC+TG GF RNLT EI+ Q+
Sbjct: 76 LLDGKQ--TEAVYMPYLDRKTICVSTMVGCPAGCAFCATGAMGFGRNLTAAEILDQVLAV 133
Query: 657 EFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYGLSRRHVIL 716
R+I N+V+MGMGEPLLNY++ + A +++L A +S R V L
Sbjct: 134 AGH---------EGISPREIRNVVLMGMGEPLLNYENVLKAARIMLHPQALAMSPRRVTL 184
Query: 717 STSGIIPMIDKLAQE-CPVELAVSLHASNNNLRNKLVPISKKYPLKELILACHRYITYSP 775
ST GI I +LA+E V LA+SLHA + R +++P + +Y + E++ A Y +
Sbjct: 185 STVGIPKGIRRLAEEDLGVRLALSLHAPDEETRQRIIPTAHRYSIAEIMAAVRHYQAVTG 244
Query: 776 RHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFNCFPNSNLICSKNSRI 835
R +T EY ML G+ND A L L+R +NLIPFN + S S ++I
Sbjct: 245 RR-VTLEYTMLKGVNDHLWQAELLADLLRG----LVSHVNLIPFNPWEGSPFQSSPRAQI 299
Query: 836 KIFAKILMNSGIFVTIRKIRGNDINAACGQLS 867
FA +L G+ V++R RG D+ AACGQL+
Sbjct: 300 LAFADVLERRGVPVSVRWSRGRDVGAACGQLA 331
>gnl|CDD|237721 PRK14466, PRK14466, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 345
Score = 262 bits (672), Expect = 1e-78
Identities = 129/341 (37%), Positives = 202/341 (59%), Gaps = 24/341 (7%)
Query: 530 KNIVHELGEMP-FRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQI 588
+++ LG MP F AKQ+ W++ V+ ++MT++S++ R+KL I A + +Q
Sbjct: 16 QSVAKRLG-MPAFAAKQIASWLYDKKVTSIDEMTNISLAHREKLAEEYEIGAYAPVDEQR 74
Query: 589 SFDGTRKWIFHVKKN-IIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVG 647
S DGT K++F V + +E+V+IPE++R TLC+S+QVGC +NC+FC TG+QGF NLT
Sbjct: 75 SVDGTIKYLFPVGEGHFVESVYIPEEDRATLCVSSQVGCKMNCLFCMTGKQGFTGNLTAA 134
Query: 648 EIIGQLWVTEFKLRREKNIKINSQGKR-QITNIVMMGMGEPLLNYKSTIGALKLILSDHA 706
+I+ Q I S +R ++TN+V MGMGEPL N + AL+++ + +
Sbjct: 135 QILNQ---------------IYSLPERDKLTNLVFMGMGEPLDNLDEVLKALEILTAPYG 179
Query: 707 YGLSRRHVILSTSGIIPMIDKLAQECPVELAVSLHASNNNLRNKLVPISKKYPLKELILA 766
YG S + + +ST G+ + + +E LA+SLH+ R +L+P K + +KE+I
Sbjct: 180 YGWSPKRITVSTVGLKKGLKRFLEESECHLAISLHSPFPEQRRELMPAEKAFSIKEIIDL 239
Query: 767 CHRYITYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFNCFPNSN 826
Y +S + ++FEY + G+ND+ HA EL+ L+R C++NLI F+ P +
Sbjct: 240 LKNY-DFSKQRRVSFEYIVFKGLNDSLKHAKELVKLLRG----IDCRVNLIRFHAIPGVD 294
Query: 827 LICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQLS 867
L S +R++ F L + G+F TIR RG DI AACG LS
Sbjct: 295 LEGSDMARMEAFRDYLTSHGVFTTIRASRGEDIFAACGMLS 335
>gnl|CDD|237717 PRK14455, PRK14455, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 356
Score = 262 bits (671), Expect = 2e-78
Identities = 131/338 (38%), Positives = 196/338 (57%), Gaps = 16/338 (4%)
Query: 535 ELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQISFDGTR 594
E GE FRA Q+ W+++ V F +MT+LS LR+KL ++ + Q S DGT
Sbjct: 27 EQGEKKFRATQIWDWLYRKRVQSFEEMTNLSKDLREKLNDNFVVTTLKTRVKQESKDGTI 86
Query: 595 KWIFHVK-KNIIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVGEIIGQL 653
K++F + +IETV + + N++C++TQVGC I C FC++ G R+L GEI+ Q+
Sbjct: 87 KFLFELPDGYLIETVLMRHEYGNSVCVTTQVGCRIGCTFCASTLGGLKRDLEAGEIVAQV 146
Query: 654 WVTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYGLSRRH 713
+ + L + +R +++IV+MG+GEP NY + + L++I D + RH
Sbjct: 147 MLVQKYL--------DETEER-VSHIVVMGIGEPFDNYDNVMDFLRIINDDKGLAIGARH 197
Query: 714 VILSTSGIIPMIDKLAQE-CPVELAVSLHASNNNLRNKLVPISKKYPLKELILACHRYIT 772
+ +STSGI P I A E + LA+SLHA NN LR+ L+PI++ YPL++L+ A YI
Sbjct: 198 ITVSTSGIAPKIYDFADEGLQINLAISLHAPNNELRSSLMPINRAYPLEKLMEAIEYYIE 257
Query: 773 YSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFNCFPNSNLICSKN 832
+ R +TFEY +L G+ND HA EL L++ K C +NLIP N P + + +
Sbjct: 258 KTNRR-VTFEYILLGGVNDQVEHAEELADLLKGIK----CHVNLIPVNPVPERDYVRTPK 312
Query: 833 SRIKIFAKILMNSGIFVTIRKIRGNDINAACGQLSGEE 870
I F L +G+ TIR+ G DI+AACGQL +E
Sbjct: 313 EDIFAFEDTLKKNGVNCTIRREHGTDIDAACGQLRAKE 350
>gnl|CDD|238396 cd00773, HisRS-like_core, Class II Histidinyl-tRNA synthetase
(HisRS)-like catalytic core domain. HisRS is a homodimer.
It is responsible for the attachment of histidine to the
3' OH group of ribose of the appropriate tRNA. This
domain is primarily responsible for ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. Class
II assignment is based upon its structure and the
presence of three characteristic sequence motifs. This
domain is also found at the C-terminus of eukaryotic GCN2
protein kinase and at the N-terminus of the ATP
phosphoribosyltransferase accessory subunit, HisZ. HisZ
along with HisG catalyze the first reaction in histidine
biosynthesis. HisZ is found only in a subset of bacteria
and differs from HisRS in lacking a C-terminal anti-codon
binding domain.
Length = 261
Score = 246 bits (631), Expect = 3e-74
Identities = 102/267 (38%), Positives = 141/267 (52%), Gaps = 42/267 (15%)
Query: 866 LSGEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMFR 925
+ D V KEMY F D+ D L+LRP+ TA V R+V EN L P +L+Y GP+FR
Sbjct: 35 FLRKSGDEVSKEMYRFKDKGGRD-LALRPDLTAPVARAVAENLLSLPLPLKLYYIGPVFR 93
Query: 926 HERPQYGRYRQFYQIGVEAIGFPGPDIDAELIIMCSRLWKNLNLKNICLELNSIGNFNER 985
+ERPQ GRYR+FYQ+GVE IG P DAE+I + + + L LK+ +++N G +
Sbjct: 94 YERPQKGRYREFYQVGVEIIGSDSPLADAEVIALAVEILEALGLKDFQIKINHRGILDGI 153
Query: 986 KKYCIDLINYIKKHKDSKWFCEDIKHSLYLNSLRVLDSKNLIIREILINAPKLLDYLEKD 1045
D YI+ +L+D L+K+
Sbjct: 154 AGLLEDREEYIE---------------------------------------RLIDKLDKE 174
Query: 1046 SLDHFYGIQKILN--YNNISYKINTKLVRGMDYYNRTVFEWTTDKLGSQNSICGGGRYDF 1103
+L H + L +I Y I+ LVRG+DYY VFE D LG+Q SI GGGRYD
Sbjct: 175 ALAHLEKLLDYLEALGVDIKYSIDLSLVRGLDYYTGIVFEAVADGLGAQGSIAGGGRYDG 234
Query: 1104 LIKKFSNKFVPASGFAIGIERLIELIK 1130
L+++F + VPA GFAIG+ERL+ ++
Sbjct: 235 LLEEFGGEDVPAVGFAIGLERLLLALE 261
>gnl|CDD|237719 PRK14462, PRK14462, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 356
Score = 249 bits (637), Expect = 9e-74
Identities = 122/351 (34%), Positives = 190/351 (54%), Gaps = 34/351 (9%)
Query: 535 ELGEM---PFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQISFD 591
EL E+ FRAKQ+ +W++ + F+ M +L LR+ L + I+ + S D
Sbjct: 12 ELSELLKPSFRAKQIYQWLYAKYATSFDDMKNLPKDLREYLAQEFTLDPLKIVKVEQSKD 71
Query: 592 GTRKWIFHVKKN-IIETVFIPEKN-------------RNTLCISTQVGCAINCIFCSTGR 637
G++K++F ++ +E V + K+ + T+C+S+QVGC + C FC T +
Sbjct: 72 GSKKYLFKLRDGHTVEAVLLKMKDEKIDEEGKILEHAKYTVCVSSQVGCKVGCAFCLTAK 131
Query: 638 QGFVRNLTVGEIIGQLWVTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGA 697
GFVRNL+ GEI+GQ+ ++++ NI KR NIV MGMGEPL N + A
Sbjct: 132 GGFVRNLSAGEIVGQILW----IKKDNNIPYE---KR--VNIVYMGMGEPLDNLDNVSKA 182
Query: 698 LKLILSDHAYGLSRRHVILSTSGIIPMIDKLAQE-CPVELAVSLHASNNNLRNKLVPISK 756
+K+ + +S R +STSG+ I KL + V+LA+SLHA ++ LR++L+PI+K
Sbjct: 183 IKIFSENDGLAISPRRQTISTSGLASKIKKLGEMNLGVQLAISLHAVDDELRSELMPINK 242
Query: 757 KYPLKELILACHRY-ITYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKIN 815
Y ++ +I A ++ I R M FEY ++ +ND A +L+ L+ K K+N
Sbjct: 243 AYNIESIIDAVRKFPIDQRKRVM--FEYLVIKDVNDDLKSAKKLVKLLNGIK----AKVN 296
Query: 816 LIPFNCFPNSNLICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQL 866
LI FN S + F L + G+ TIR+ +G DI+AACGQL
Sbjct: 297 LILFNPHEGSKFERPSLEDMIKFQDYLNSKGLLCTIRESKGLDISAACGQL 347
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 241 bits (619), Expect = 1e-73
Identities = 87/174 (50%), Positives = 124/174 (71%), Gaps = 2/174 (1%)
Query: 181 EYIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGI 240
+ IK+AI+G+PNVGKS+L+N+LLGE RVI D GTTRDSI FEY+ +KY LIDTAGI
Sbjct: 1 DPIKIAIIGRPNVGKSSLLNALLGEERVIVSDIAGTTRDSIDVPFEYDGQKYTLIDTAGI 60
Query: 241 RRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCV 300
R++ K E IEK+SV++TLK+I A+VV+L+LDA + I+ QD+ IA I E G++LI+ V
Sbjct: 61 RKKGKVTEGIEKYSVLRTLKAIERADVVLLVLDASEGITEQDLRIAGLILEEGKALIIVV 120
Query: 301 NKWDSIIHNQ--RKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESINHVY 352
NKWD + ++ K + +++KL FL +A FISA+ ++ ++I VY
Sbjct: 121 NKWDLVEKDEKTMKEFEKELRRKLPFLDYAPIVFISALTGQGVDKLFDAIKEVY 174
Score = 103 bits (260), Expect = 3e-25
Identities = 45/169 (26%), Positives = 81/169 (47%), Gaps = 12/169 (7%)
Query: 5 LVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGF--EP 62
+ ++GRPNVGKS+L N L +V++ G TRD + + +IDT G +
Sbjct: 5 IAIIGRPNVGKSSLLNALLGEERVIVSDIAGTTRDSIDVPFEYDGQKYTLIDTAGIRKKG 64
Query: 63 EVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSE 122
+V +GI +T +AI +D+++ ++D +G+ EQD I + + G+ +++V+NK +
Sbjct: 65 KVTEGIEKYSVLRTLKAIERADVVLLVLDASEGITEQDLRIAGLILEEGKALIIVVNKWD 124
Query: 123 NINSS----------ISLDFYELGIGNPHIISALYGNGIKNFLENILTI 161
+ + L ISAL G G+ + I +
Sbjct: 125 LVEKDEKTMKEFEKELRRKLPFLDYAPIVFISALTGQGVDKLFDAIKEV 173
>gnl|CDD|172932 PRK14456, PRK14456, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 368
Score = 239 bits (611), Expect = 4e-70
Identities = 140/371 (37%), Positives = 196/371 (52%), Gaps = 26/371 (7%)
Query: 508 GDTDPIKAAKGTIRADFAESIDKNIVHELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMS 567
T +K IR + ++ LGE +RA QL +W+ F +MT LS
Sbjct: 8 EKTHTMKKELQNIR-NLRRQELTELLARLGEPAWRAAQLHQWLFSHRALSFEEMTTLSKP 66
Query: 568 LRKKLKNSVYIKAPHIMSDQISFDG-----TRKWIFHVKKN-IIETVFIPEKNRNTLCIS 621
LR+KL S I+ P + +G T K + + ++ETV IP R T CIS
Sbjct: 67 LRRKLAESFAIQPPVTEKHDETMEGSPAGPTEKLLIKLPDGELVETVLIPGPERMTACIS 126
Query: 622 TQVGCAINCIFCSTGRQGFVRNLTVGEIIGQLWVTEFKLRREKNIKINSQGKRQITNIVM 681
+Q GCA+ C FC+TG+ GF RNLT GEI GQ++ + E+N +R ITNIV
Sbjct: 127 SQAGCALRCSFCATGQMGFRRNLTAGEITGQVFALS-DMLAERN------RERGITNIVF 179
Query: 682 MGMGEPLLNYKSTIGA-LKLILSDHAYGLSRRHVILSTSGIIPMIDKLAQE-CPVELAVS 739
MGMGEPLLN + A L L + + +S+R + +ST GI P ID+LA +LAVS
Sbjct: 180 MGMGEPLLNTDNVFEAVLTLSTRKYRFSISQRKITISTVGITPEIDRLATSGLKTKLAVS 239
Query: 740 LHASNNNLRNKLVPI-SKKYPLKEL--ILACHRYITYSPRHMITFEYCMLHGINDTDIHA 796
LH+++ R +L+P ++ YPL EL L + T P +T Y +L GIND+ A
Sbjct: 240 LHSADQEKRERLMPQAARDYPLDELREALIGYASKTGEP---VTLVYMLLEGINDSPEDA 296
Query: 797 IELISLMRKNKILTSCKINLIPFNCFPNSNLICSKNSRIKIFAKILMNSGIFVTIRKIRG 856
+LI + CKINLI +N N +S + F L+++G+ VT+RK G
Sbjct: 297 RKLIRFASR----FFCKINLIDYNSIVNIKFEPVCSSTRERFRDRLLDAGLQVTVRKSYG 352
Query: 857 NDINAACGQLS 867
INAACGQL+
Sbjct: 353 TTINAACGQLA 363
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 157
Score = 222 bits (569), Expect = 4e-67
Identities = 83/155 (53%), Positives = 111/155 (71%), Gaps = 2/155 (1%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGFEPEVK 65
+VGRPNVGKSTLFNRLT RDA+V++ PG+TRDR YGE G + FI+IDTGG EP+
Sbjct: 1 AIVGRPNVGKSTLFNRLTGRRDAIVSDTPGVTRDRKYGEAEWGGREFILIDTGGIEPD-D 59
Query: 66 KGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSENIN 125
+GI E+ +Q + AI E+D+I+F+VDGR+GL D+ I +LRKS +P++LV+NK +NI
Sbjct: 60 EGISKEIREQAEIAIEEADVILFVVDGREGLTPADEEIAKYLRKSKKPVILVVNKIDNIK 119
Query: 126 SSISL-DFYELGIGNPHIISALYGNGIKNFLENIL 159
+FY LG G P ISA +G GI + L+ IL
Sbjct: 120 EEEEAAEFYSLGFGEPIPISAEHGRGIGDLLDAIL 154
Score = 129 bits (328), Expect = 9e-35
Identities = 49/121 (40%), Positives = 72/121 (59%), Gaps = 3/121 (2%)
Query: 186 AIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRRRNK 245
AIVG+PNVGKSTL N L G I DTPG TRD E+ +++ILIDT GI
Sbjct: 1 AIVGRPNVGKSTLFNRLTGRRDAIVSDTPGVTRDRKYGEAEWGGREFILIDTGGI---EP 57
Query: 246 TFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCVNKWDS 305
E I K + +I EA+V++ ++D ++ ++ D IA ++ +S + +I+ VNK D+
Sbjct: 58 DDEGISKEIREQAEIAIEEADVILFVVDGREGLTPADEEIAKYLRKSKKPVILVVNKIDN 117
Query: 306 I 306
I
Sbjct: 118 I 118
>gnl|CDD|184685 PRK14453, PRK14453, chloramphenicol/florfenicol resistance protein;
Provisional.
Length = 347
Score = 197 bits (502), Expect = 1e-55
Identities = 123/352 (34%), Positives = 181/352 (51%), Gaps = 32/352 (9%)
Query: 530 KNIVHELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKN----SVYIKAP--HI 583
K I+ L +R +Q+ K I K + +F M L +LR+ L N +V P
Sbjct: 11 KQILSNLKLPDYRYEQITKAIFKQRIDNFEDMHILPKALRESLINEFGKNVLSVIPVFEQ 70
Query: 584 MSDQISFDGTRKWIFHVKKN-IIETVFIP-EKNRNTLCISTQVGCAINCIFCSTGRQGFV 641
S Q++ K +F + IE V + ++ + CIS+Q GC C FC+TG G
Sbjct: 71 DSKQVT-----KVLFELTDGERIEAVGLKYKQGWESFCISSQCGCGFGCRFCATGSIGLK 125
Query: 642 RNLTVGEIIGQLWVTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLI 701
RNLT EI QL F L +++S I MGMGE L N ALK++
Sbjct: 126 RNLTADEITDQLLY--FYL---NGHRLDS--------ISFMGMGEALAN-PELFDALKIL 171
Query: 702 LSDHAYGLSRRHVILSTSGIIPMIDKLAQECP-VELAVSLHASNNNLRNKLVPISKKYPL 760
+ +GLS+R + +ST GIIP I +L QE P V L SLH+ + R++L+PI+K++PL
Sbjct: 172 TDPNLFGLSQRRITISTIGIIPGIQRLTQEFPQVNLTFSLHSPFESQRSELMPINKRFPL 231
Query: 761 KELILACHRYITYSPRHMITFEYCMLHGINDTDIHAIELISLMRKN-KILTSCKINLIPF 819
E++ +I ++ R + Y ML G+ND+ HA ++ L+R +NLIP+
Sbjct: 232 NEVMKTLDEHIRHTGRK-VYIAYIMLEGVNDSKEHAEAVVGLLRNRGSWEHLYHVNLIPY 290
Query: 820 NCFPNS--NLICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQLSGE 869
N + S +IK F L ++GI VT+R G+DI+AACGQL G
Sbjct: 291 NSTDKTPFKFQSSSAGQIKQFCSTLKSAGISVTVRTQFGSDISAACGQLYGN 342
>gnl|CDD|179085 PRK00668, ndk, mulitfunctional nucleoside diphosphate
kinase/apyrimidinic endonuclease/3'-; Validated.
Length = 134
Score = 188 bits (481), Expect = 1e-55
Identities = 63/113 (55%), Positives = 83/113 (73%), Gaps = 2/113 (1%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
RTFS+I DA+++ ++GEI +R+EK GLKI+A M +LS+ E Y+ HK +PFF LV
Sbjct: 3 RTFSIIKPDAVQRGLIGEIISRFEKKGLKIVALKMMQLSRELAEGHYAEHKEKPFFGELV 62
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAAKGTIRADFAESIDKNIVH 534
FM SGPV + VLEGE+AI K R L+G T+P +AA GTIR DFA SI +N+VH
Sbjct: 63 EFMTSGPVVVMVLEGENAIAKVRELMGATNPAEAAPGTIRGDFALSIGENVVH 115
>gnl|CDD|172940 PRK14465, PRK14465, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 342
Score = 179 bits (455), Expect = 1e-49
Identities = 109/340 (32%), Positives = 181/340 (53%), Gaps = 22/340 (6%)
Query: 532 IVHELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQISFD 591
I+ LGE FRAKQ+ ++ +++ T S +++KL+ + ++ D S D
Sbjct: 18 IMVSLGEKKFRAKQIYHGLYVNRYETWDQFTTFSKEVKEKLEELCSLTELEVVKDLKSVD 77
Query: 592 GTRKWIFHVKKNI-IETVFIPEKN--RNTLCISTQVGCAINCIFCSTGRQGFVRNLTVGE 648
GT+K+ F+ + E V+IP + R T+CIS+Q+GC +NC FC+T + F NL E
Sbjct: 78 GTQKFTFYSGEGKEFEAVWIPSGDGGRKTICISSQIGCTLNCKFCATAKLEFQGNLKAHE 137
Query: 649 IIGQLWVTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYG 708
I+ Q+ L+ EK + + TN+V MGMGEP+ NY + I A ++ A+
Sbjct: 138 IVDQV------LQVEKIVGDRA------TNVVFMGMGEPMHNYFNVIRAASILHDPDAFN 185
Query: 709 LSRRHVILSTSGIIPMIDKLAQ-ECPVELAVSLHASNNNLRNKLVPISKKYPLKELILAC 767
L + + +STSG++ I + + + P A+SL+ + N R +++ I +K+PL+EL+ A
Sbjct: 186 LGAKRITISTSGVVNGIRRFIENKEPYNFAISLNHPDPNGRLQIMDIEEKFPLEELLQAA 245
Query: 768 HRYITYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFNCFPNSNL 827
+ T + ITFEY M+ G+N +A +L+ + R CKIN+IP N
Sbjct: 246 KDF-TRELKRRITFEYVMIPGVNMGRENANKLVKIARS----LDCKINVIPLNT-EFFGW 299
Query: 828 ICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQLS 867
+ + F +L +G+ + R+ G DI ACG L+
Sbjct: 300 RRPTDDEVAEFIMLLEPAGVPILNRRSPGKDIFGACGMLA 339
>gnl|CDD|223183 COG0105, Ndk, Nucleoside diphosphate kinase [Nucleotide transport
and metabolism].
Length = 135
Score = 167 bits (426), Expect = 3e-48
Identities = 59/114 (51%), Positives = 79/114 (69%), Gaps = 2/114 (1%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
RT S+I DA+++ ++GEI +R+EK GLKI+A M +LS+ E Y+ HK +PFF LV
Sbjct: 4 RTLSIIKPDAVKRGLIGEIISRFEKKGLKIVALKMVQLSRELAENHYAEHKGKPFFGELV 63
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAAKGTIRADFAESIDKNIVHE 535
F+ SGPV VLEGE+AI R L+G T+P AA GTIR DFA S+ +N+VH
Sbjct: 64 EFITSGPVVAMVLEGENAISVVRKLMGATNPANAAPGTIRGDFALSVGENVVHG 117
>gnl|CDD|239876 cd04413, NDPk_I, Nucleoside diphosphate kinase Group I
(NDPk_I)-like: NDP kinase domains are present in a large
family of structurally and functionally conserved
proteins from bacteria to humans that generally catalyze
the transfer of gamma-phosphates of a nucleoside
triphosphate (NTP) donor onto a nucleoside diphosphate
(NDP) acceptor through a phosphohistidine intermediate.
The mammalian nm23/NDP kinase gene family can be divided
into two distinct groups. The group I genes encode
proteins that generally have highly homologous
counterparts in other organisms and possess the classic
enzymatic activity of a kinase. This group includes
vertebrate NDP kinases A-D (Nm23- H1 to -H4), and its
counterparts in bacteria, archea and other eukaryotes.
NDP kinases exist in two different quaternary
structures; all known eukaryotic enzymes are hexamers,
while some bacterial enzymes are tetramers, as in
Myxococcus. They possess the NDP kinase active site
motif (NXXH[G/A]SD) and the nine residues that are most
essential for catalysis.
Length = 130
Score = 167 bits (425), Expect = 4e-48
Identities = 58/113 (51%), Positives = 79/113 (69%), Gaps = 2/113 (1%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
RT +I D +++ ++GEI +R+E+ GLKI+A M +L++ E+ Y+ HK +PFF LV
Sbjct: 2 RTLVIIKPDGVQRGLIGEIISRFERKGLKIVALKMLQLTEELAEEHYAEHKGKPFFPELV 61
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAAKGTIRADFAESIDKNIVH 534
FM SGPV VLEGE+A+K R L+G T+P AA GTIR DFA SI +NIVH
Sbjct: 62 EFMTSGPVVAMVLEGENAVKTVRKLMGATNPADAAPGTIRGDFALSIGRNIVH 114
>gnl|CDD|201162 pfam00334, NDK, Nucleoside diphosphate kinase.
Length = 135
Score = 166 bits (424), Expect = 6e-48
Identities = 57/113 (50%), Positives = 78/113 (69%), Gaps = 2/113 (1%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
RT +I DA+++ ++GEI +R+EK G KI+A M +L++ E+ Y+ HK +PFF LV
Sbjct: 2 RTLVIIKPDAVQRGLIGEIISRFEKKGFKIVALKMLQLTREQAEEHYAEHKGKPFFPGLV 61
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAAKGTIRADFAESIDKNIVH 534
FM SGPV VLEGE+A+ R L+G T+P +AA GTIR DFA SI +N VH
Sbjct: 62 EFMTSGPVVAMVLEGENAVSVVRELMGATNPAEAAPGTIRGDFAVSIGRNAVH 114
>gnl|CDD|197791 smart00562, NDK, Enzymes that catalyze nonsubstrate specific
conversions of nucleoside diphosphates to nucleoside
triphosphates. These enzymes play important roles in
bacterial growth, signal transduction and pathogenicity.
Length = 135
Score = 155 bits (395), Expect = 4e-44
Identities = 57/113 (50%), Positives = 80/113 (70%), Gaps = 2/113 (1%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
RT ++I DA+++ ++GEI +R+E+ G KI+A M +L++ E+FY+ H+ +PFF +LV
Sbjct: 2 RTLAIIKPDAVQRGLIGEIISRFERKGFKIVAMKMLQLTEEQAEEFYAEHEGKPFFNDLV 61
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAAKGTIRADFAESIDKNIVH 534
FM SGPV VLEGEDA+K R L+G TDP +AA GTIR DF I +N VH
Sbjct: 62 EFMTSGPVVAMVLEGEDAVKTWRTLMGPTDPREAAPGTIRGDFGLDIGRNAVH 114
>gnl|CDD|172945 PRK14470, PRK14470, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 336
Score = 149 bits (378), Expect = 2e-39
Identities = 86/282 (30%), Positives = 132/282 (46%), Gaps = 24/282 (8%)
Query: 591 DGTRKWIFHVKKNI-IETVFIP-EKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVGE 648
DG RK++F + + +E V IP + +C+S+Q GCA+ C FC+TG+ G R+L E
Sbjct: 70 DGFRKYLFELPDGLRVEAVRIPLFDTHHVVCLSSQAGCALGCAFCATGKLGLDRSLRSWE 129
Query: 649 IIGQLWVTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYG 708
I+ QL + + + +R IT +V MG GEP LNY + A +
Sbjct: 130 IVAQL------------LAVRADSERPITGVVFMGQGEPFLNYDEVLRAAYALCDPAGAR 177
Query: 709 LSRRHVILSTSGIIPMIDKLAQEC-PVELAVSLHASNNNLRNKLVPISKKYPLKELILAC 767
+ R + +ST+G++PMI + E L +SL+A+ R L+PI + +PL EL+ A
Sbjct: 178 IDGRRISISTAGVVPMIRRYTAEGHKFRLCISLNAAIPWKRRALMPIEQGFPLDELVEAI 237
Query: 768 HRYITYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINLIPFNCFPNSNL 827
+ R +T EY M+ G+N + A L L+ + ++N I N
Sbjct: 238 REHAALRGR--VTLEYVMISGVNVGEEDAAALGRLLAGIPV----RLNPIAVND-ATGRY 290
Query: 828 ICSKNSRIKIFAKILMNS--GIFVTIRKIRGNDINAACGQLS 867
F L G V R G D +AACG L+
Sbjct: 291 RPPDEDEWNAFRDALARELPGTPVVRRYSGGQDEHAACGMLA 332
>gnl|CDD|184691 PRK14464, PRK14464, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 344
Score = 144 bits (364), Expect = 2e-37
Identities = 86/275 (31%), Positives = 138/275 (50%), Gaps = 37/275 (13%)
Query: 605 IETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQGFVRNLTVGEIIGQLWVTEFKLRREK 664
+E+V +P R+ LC+STQVGCA+ C+FC TGR G +R L EI+ Q+ L R
Sbjct: 88 VESVLLP---RDGLCVSTQVGCAVGCVFCMTGRSGLLRQLGSAEIVAQV-----VLAR-- 137
Query: 665 NIKINSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYGLSRRHVILSTSGIIPM 724
+R + +V MGMGEP N + + A+ L+ ++ G ++++ ST G +
Sbjct: 138 -------RRRAVKKVVFMGMGEPAHNLDNVLEAIDLLGTEGGIG--HKNLVFSTVGDPRV 188
Query: 725 IDKLAQECPVE--LAVSLHASNNNLRNKLVPISKKYPLKELILACHRY--ITYSPRHMIT 780
++L Q+ V+ LA+SLH + LR +L+P + + +EL+ Y T P I
Sbjct: 189 FERLPQQ-RVKPALALSLHTTRAELRARLLPRAPRIAPEELVELGEAYARATGYP---IQ 244
Query: 781 FEYCMLHGINDTDIHAIELISLMRKNKILTSCK---INLIPFNCFPNSNLICSKNSRIKI 837
+++ +L G+ND+D E+ ++R L K +NLIP+N RI
Sbjct: 245 YQWTLLEGVNDSD---EEMDGIVR----LLKGKYAVMNLIPYNSVDGDAYRRPSGERIVA 297
Query: 838 FAKILMNSGIFVTIRKIRGNDINAACGQLSGEETD 872
A+ L G+ +R G D++ CGQL
Sbjct: 298 MARYLHRRGVLTKVRNSAGQDVDGGCGQLRARAAK 332
>gnl|CDD|232978 TIGR00443, hisZ_biosyn_reg, ATP phosphoribosyltransferase, regulatory
subunit. Apparant second copies of histidyl-tRNA
synthetase, found in Bacillus subtilis, Synechocystis
sp., Aquifex aeolicus, and others, are in fact a
regulatory subunit of ATP phosphoribosyltransferase, and
usually encoded by a gene adjacent to that encoding the
catalytic subunit [Amino acid biosynthesis, Histidine
family].
Length = 313
Score = 141 bits (359), Expect = 5e-37
Identities = 83/281 (29%), Positives = 128/281 (45%), Gaps = 37/281 (13%)
Query: 873 IVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMFRHERPQYG 932
I+ ++++ D+L G L LRP+ TA + R V P RL Y+G +FR G
Sbjct: 47 ILNEDLFKLFDQL-GRVLGLRPDMTAPIARLVSTRLRDRPLPLRLCYAGNVFRTNESGGG 105
Query: 933 RYRQFYQIGVEAIGFPGPDIDAELIIMCSRLWKNLNLKNICLELNSIGNFNERKKYCIDL 992
R R+F Q GVE IG GP DAE+I + K L LK+ +EL +G
Sbjct: 106 RSREFTQAGVELIGAGGPAADAEVIALLIEALKALGLKDFKIELGHVGLVRA-------- 157
Query: 993 INYIKKHKDSKWFCEDIKHSLY---LNSL-RVLDSKNL--IIREILINAPKL-------L 1039
+++ + E ++ +L L +L ++ L +RE L+ P+L L
Sbjct: 158 --LLEEAGLPEEAREALREALARKDLVALEELVAELGLSPEVRERLLALPRLRGDGEEVL 215
Query: 1040 DYLEKD--------SLDHFYGIQKILN--YNNISYKINTKLVRGMDYYNRTVFEWTTDKL 1089
+ +LD + ++L ++ LVRG YY +FE L
Sbjct: 216 EEARALAGSETAEAALDELEAVLELLEARGVEEYISLDLGLVRGYHYYTGLIFEGYAPGL 275
Query: 1090 GSQNSICGGGRYDFLIKKFSNKFVPASGFAIGIERLIELIK 1130
G + GGGRYD L+ +F PA+GFA+ +ERL+E +
Sbjct: 276 G--APLAGGGRYDELLGRFGRPL-PATGFALNLERLLEALT 313
>gnl|CDD|237043 PRK12292, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 391
Score = 142 bits (361), Expect = 2e-36
Identities = 96/331 (29%), Positives = 150/331 (45%), Gaps = 44/331 (13%)
Query: 866 LSGEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMFR 925
L I+ + +D+L+G L LRP+ TA + R GP RL Y+G +FR
Sbjct: 50 LLAGGGAILDLRTFKLVDQLSGRTLGLRPDMTAQIARIAATRLANRPGPLRLCYAGNVFR 109
Query: 926 HERPQYGRYRQFYQIGVEAIGFPGPDIDAELIIMCSRLWKNLNLKNICLELNSIGNFNER 985
+ GR R+F Q GVE IG G + DAE+I++ K L L N L+L +G F
Sbjct: 110 AQERGLGRSREFLQSGVELIGDAGLEADAEVILLLLEALKALGLPNFTLDLGHVGLFRA- 168
Query: 986 KKYCIDLINYIKKHKDSKWFCEDIKHSLY---LNSLRVL------DSKNLII-------- 1028
L+ ++ + E ++ +L +L L + ++ ++
Sbjct: 169 ------LLEAAGLSEELE---EVLRRALANKDYVALEELVLDLSEELRDALLALPRLRGG 219
Query: 1029 REILINAPKLLDYLE-KDSLDHFYGIQKILN-YNNISYKINTKL----VRGMDYYNRTVF 1082
RE+L A KLL L K +LD ++ + Y I L +R +DYY VF
Sbjct: 220 REVLEEARKLLPSLPIKRALDE---LEALAEALEKYGYGIPLSLDLGLLRHLDYYTGIVF 276
Query: 1083 EWTTDKLGSQNSICGGGRYDFLIKKFSNKFVPASGFAIGIERLIELIKKININHNFSHQC 1142
E D G N I GGRYD L+ +F + PA+GF++ ++RL+EL ++ +
Sbjct: 277 EGYVD--GVGNPIASGGRYDDLLGRF-GRARPATGFSLDLDRLLELQLELPVE-----AR 328
Query: 1143 DIYIVHVGKEAELKAFVLSENLRTLGLKVIL 1173
++ EA A ++ LR G V+L
Sbjct: 329 KDLVIAPDSEALAAALAAAQELRKKGEIVVL 359
>gnl|CDD|173387 PTZ00093, PTZ00093, nucleoside diphosphate kinase, cytosolic;
Provisional.
Length = 149
Score = 125 bits (315), Expect = 4e-33
Identities = 46/113 (40%), Positives = 74/113 (65%), Gaps = 2/113 (1%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
RTF ++ D +++ +VGEI R+EK G K++A M + + E+ Y HK +PFF LV
Sbjct: 4 RTFIMVKPDGVQRGLVGEIIKRFEKKGYKLVALKMLQPTPEIAEEHYKEHKGKPFFPGLV 63
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAAKGTIRADFAESIDKNIVH 534
++ SGPV V EG++ +K+ R L+G T+P+++A GTIR DF + +N++H
Sbjct: 64 KYISSGPVVCMVWEGKNVVKQGRKLLGATNPLESAPGTIRGDFCVDVGRNVIH 116
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 123 bits (311), Expect = 5e-33
Identities = 50/116 (43%), Positives = 70/116 (60%), Gaps = 2/116 (1%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGFEPEVK 65
LVGRPNVGKSTL N LT ++ A+V++YPG TRD G + I++DT G
Sbjct: 3 ALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGV-LGLGRQIILVDTPGLIEGAS 61
Query: 66 KGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQ-PIVLVINK 120
+G E + +AI E+D+I+ +VD +GL E D+ I L K + PI+LV+NK
Sbjct: 62 EGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPKKPIILVLNK 117
Score = 117 bits (296), Expect = 5e-31
Identities = 43/120 (35%), Positives = 72/120 (60%), Gaps = 4/120 (3%)
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRRR 243
+VA+VG+PNVGKSTLIN+L G I D PGTTRD I + ++ IL+DT G+
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLGL-GRQIILVDTPGLIEG 59
Query: 244 NKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYES-GRSLIVCVNK 302
+ +E + L++I EA++++L++DA + ++ D I + + + +I+ +NK
Sbjct: 60 ASEGKGVE--GFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPKKPIILVLNK 117
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 124 bits (313), Expect = 1e-32
Identities = 56/166 (33%), Positives = 87/166 (52%), Gaps = 15/166 (9%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRR 242
IKV I GKPNVGKS+L+N+L G +R I D GTTRD I+ + LIDTAG+R
Sbjct: 4 IKVVIAGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEEEIDLGGIPVRLIDTAGLR- 62
Query: 243 RNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCVNK 302
+T + IEK + + ++I EA++V+L++DA + + +D+ I + + +IV +NK
Sbjct: 63 --ETEDEIEKIGIERAREAIEEADLVLLVVDASEGLDEEDLEILELP--AKKPVIVVLNK 118
Query: 303 WDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESI 348
D + + N ISA I+ E++
Sbjct: 119 SDLLSDAEGISELNGKP----------IIAISAKTGEGIDELKEAL 154
Score = 104 bits (261), Expect = 1e-25
Identities = 54/161 (33%), Positives = 87/161 (54%), Gaps = 13/161 (8%)
Query: 5 LVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGF---E 61
+V+ G+PNVGKS+L N L A+V++ G TRD E +G +IDT G E
Sbjct: 6 VVIAGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEEEIDLGGIPVRLIDTAGLRETE 65
Query: 62 PEV-KKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINK 120
E+ K GI ++ ++AI E+D+++ +VD +GL E+D I + +P+++V+NK
Sbjct: 66 DEIEKIGI-----ERAREAIEEADLVLLVVDASEGLDEEDLEI--LELPAKKPVIVVLNK 118
Query: 121 SENINSSISLDFYELGIGNPHIISALYGNGIKNFLENILTI 161
S+ ++ + EL ISA G GI E +L +
Sbjct: 119 SDLLSDAE--GISELNGKPIIAISAKTGEGIDELKEALLEL 157
>gnl|CDD|238335 cd00595, NDPk, Nucleoside diphosphate kinases (NDP kinases, NDPks):
NDP kinases, responsible for the synthesis of nucleoside
triphosphates (NTPs), are involved in numerous
regulatory processes associated with proliferation,
development, and differentiation. They are vital for
DNA/RNA synthesis, cell division, macromolecular
metabolism and growth. The enzymes generate NTPs or
their deoxy derivatives by terminal (gamma)
phosphotransfer from an NTP such as ATP or GTP to any
nucleoside diphosphate (NDP) or its deoxy derivative.
The sequence of NDPk has been highly conserved through
evolution. There is a single histidine residue conserved
in all known NDK isozymes, which is involved in the
catalytic mechanism. The first confirmed metastasis
suppressor gene was the NDP kinase protein encoded by
the nm23 gene. Unicellular organisms generally possess
only one gene encoding NDP kinase, while most
multicellular organisms possess not only an ortholog
that provides most of the NDP kinase enzymatic activity
but also multiple divergent paralogous genes. The human
genome codes for at least nine NDP kinases and can be
classified into two groups, Groups I and II, according
to their genomic architecture and distinct enzymatic
activity. Group I isoforms (A-D) are well-conserved,
catalytically active, and share 58-88% identity between
each other, while Group II are more divergent, with only
NDPk6 shown to be active. NDP kinases exist in two
different quaternary structures; all known eukaryotic
enzymes are hexamers, while some bacterial enzymes are
tetramers, as in Myxococcus. The hexamer can be viewed
as trimer of dimers, while tetramers are dimers of
dimers, with the dimerization interface conserved.
Length = 133
Score = 119 bits (300), Expect = 2e-31
Identities = 49/116 (42%), Positives = 72/116 (62%), Gaps = 5/116 (4%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
RT +LI DA+ + ++GEI R E G +I+A L++ E+FY HK RPFF +LV
Sbjct: 2 RTLALIKPDAVAEGLLGEIIMRIEDAGFEIVAMKELHLTEEQAEEFYVEHKGRPFFPDLV 61
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKA---AKGTIRADFAESIDKNIVH 534
FM SGPV +LE ++A+ + R ++G T+P A A G++RADF + +N VH
Sbjct: 62 QFMSSGPVVAMILEKDNAVGEWREMLGPTNPEIARHLAPGSLRADFGTDVLRNAVH 117
>gnl|CDD|222097 pfam13393, tRNA-synt_His, Histidyl-tRNA synthetase. This is a family
of class II aminoacyl-tRNA synthetase-like and ATP
phosphoribosyltransferase regulatory subunits.
Length = 308
Score = 122 bits (308), Expect = 3e-30
Identities = 68/275 (24%), Positives = 112/275 (40%), Gaps = 43/275 (15%)
Query: 876 KEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMFRHERPQYGRYR 935
+ + +D+ +G L LR + T V R + + L P RL Y+GP+ R G R
Sbjct: 52 DQTFKLVDQ-SGRLLGLRADITPQVAR-IDAHRLNRPRPLRLCYAGPVLRTRPDGLGGSR 109
Query: 936 QFYQIGVEAIGFPGPDIDAELIIMCSRLWKNLNLKNICLELNSIGNFN------------ 983
+ QIG E IG G + DAE+I + ++L +K + L+L +G
Sbjct: 110 EPLQIGAELIGHAGIEADAEVISLLLEALESLGVKGVTLDLGHVGIVRALLEALGLSEAQ 169
Query: 984 --------ERKKYCIDLINYIKKHKDSKWFCEDIKHSLYLN-SLRVLDSKNLIIREILIN 1034
+RK +L + + + + L VLD E+L
Sbjct: 170 EEALRDALQRKDL-PELEELLAELGLDPALADALLALPELYGDPEVLDEA----LELLPG 224
Query: 1035 APK--LLDYLEKDSLDHFYGIQKILN--YNNISYKINTKLVRGMDYYNRTVFEWTTDKLG 1090
+P LD LE + +L + ++ +RG +YY VF G
Sbjct: 225 SPAAAALDELEA--------LAALLEALGPGVRLTLDLAELRGYEYYTGLVFAAYAPGAG 276
Query: 1091 SQNSICGGGRYDFLIKKFSNKFVPASGFAIGIERL 1125
++ GGRYD L + F + PA+GF++ ++ L
Sbjct: 277 Q--ALARGGRYDNLGEVF-GRARPATGFSLDLDAL 308
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 123 bits (311), Expect = 2e-29
Identities = 56/204 (27%), Positives = 95/204 (46%), Gaps = 23/204 (11%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRR 242
+KV I+G+PNVGKS+L+N+LLG +R I D GTTRD I+ N L+DTAGIR
Sbjct: 218 LKVVIIGRPNVGKSSLLNALLGRDRAIVTDIAGTTRDVIEEDINLNGIPVRLVDTAGIR- 276
Query: 243 RNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCVNK 302
+T +V+E+ + + K+I EA++V+ +LDA Q + +D+ + + + +IV +NK
Sbjct: 277 --ETDDVVERIGIERAKKAIEEADLVLFVLDASQPLDKEDLALIELL-PKKKPIIVVLNK 333
Query: 303 WDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIK-------LNNINSFMESINHVYDSS 355
D + ++ ++ + +S ISA I +
Sbjct: 334 AD--LVSKIELESEKLANGDAIIS------ISAKTGEGLDALREAIKQLFGKGLGNQEGL 385
Query: 356 II----HLSTSRITRALISAIKNH 375
+ H+ +
Sbjct: 386 FLSNLRHIQLLEQAAEHLEDALQQ 409
Score = 104 bits (261), Expect = 3e-23
Identities = 55/164 (33%), Positives = 91/164 (55%), Gaps = 16/164 (9%)
Query: 5 LVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGY--IGKKSFIIIDTGGF-- 60
+V++GRPNVGKS+L N L A+V + G TRD E + ++DT G
Sbjct: 220 VVIIGRPNVGKSSLLNALLGRDRAIVTDIAGTTRD--VIEEDINLNGIPVRLVDTAGIRE 277
Query: 61 -EPEVKK-GIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVI 118
+ V++ GI ++ K+AI E+D+++F++D Q L ++D + L K +PI++V+
Sbjct: 278 TDDVVERIGI-----ERAKKAIEEADLVLFVLDASQPLDKEDLALIELLPK-KKPIIVVL 331
Query: 119 NKSENINSSISLDFYELGIGNPHI-ISALYGNGIKNFLENILTI 161
NK++ + S I L+ +L G+ I ISA G G+ E I +
Sbjct: 332 NKAD-LVSKIELESEKLANGDAIISISAKTGEGLDALREAIKQL 374
>gnl|CDD|184734 PRK14545, PRK14545, nucleoside diphosphate kinase; Provisional.
Length = 139
Score = 111 bits (280), Expect = 1e-28
Identities = 49/113 (43%), Positives = 72/113 (63%), Gaps = 2/113 (1%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
RTF++I DA+E +G I + G +I+A + +L+ D E FY++H RPF+ LV
Sbjct: 5 RTFTMIKPDAVENGHIGGILDMITAAGFRIVAMKLTQLTVADAETFYAVHAERPFYGELV 64
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAAKGTIRADFAESIDKNIVH 534
FM GP+ +LE E+A++ R LIG T+P AA+GTIR +A+SI +N VH
Sbjct: 65 EFMSRGPIVAAILEKENAVEDFRTLIGATNPADAAEGTIRKKYAKSIGENAVH 117
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 118 bits (299), Expect = 4e-28
Identities = 61/198 (30%), Positives = 99/198 (50%), Gaps = 22/198 (11%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRR 242
+KV I G+PNVGKS+L+N+LLGE R I D GTTRD I+ + LIDTAGIR
Sbjct: 216 LKVVIAGRPNVGKSSLLNALLGEERAIVTDIAGTTRDVIEEHINLDGIPLRLIDTAGIR- 274
Query: 243 RNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCVNK 302
+T + +EK + ++ ++I EA++V+L+LDA + ++ +D I + +IV +NK
Sbjct: 275 --ETDDEVEKIGIERSREAIEEADLVLLVLDASEPLTEEDDEI--LEELKDKPVIVVLNK 330
Query: 303 ------WDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESINHVYDSSI 356
D N + +I+ + K I ++ I +
Sbjct: 331 ADLTGEIDLEEENGKPVIRISAKTGEG---------IDELR-EAIKELAFGGFGGNQEGV 380
Query: 357 IHLSTSRITRALISAIKN 374
L+ +R AL A+++
Sbjct: 381 F-LTNARHLEALERALEH 397
Score = 106 bits (268), Expect = 4e-24
Identities = 53/164 (32%), Positives = 84/164 (51%), Gaps = 20/164 (12%)
Query: 5 LVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGY--IGKKSFIIIDTGGF-- 60
+V+ GRPNVGKS+L N L A+V + G TRD E + + +IDT G
Sbjct: 218 VVIAGRPNVGKSSLLNALLGEERAIVTDIAGTTRD--VIEEHINLDGIPLRLIDTAGIRE 275
Query: 61 -EPEVKK-GIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVI 118
+ EV+K GI +++++AI E+D+++ ++D + L E+D I +P+++V+
Sbjct: 276 TDDEVEKIGI-----ERSREAIEEADLVLLVLDASEPLTEEDDEI--LEELKDKPVIVVL 328
Query: 119 NKSENINSSISLDFYELGIGNPHI-ISALYGNGIKNFLENILTI 161
NK++ E G P I ISA G GI E I +
Sbjct: 329 NKADLTGEIDL----EEENGKPVIRISAKTGEGIDELREAIKEL 368
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 109 bits (275), Expect = 1e-27
Identities = 47/163 (28%), Positives = 76/163 (46%), Gaps = 10/163 (6%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYI-GKKSFIIIDTGGFEPEV 64
+ GRPNVGKS+L N L +V+ PG TRD E + ++IDT G + E
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDEEG 60
Query: 65 KKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSENI 124
G ++ +Q +D+++ +VD VE++ + LR+ G+P++LV+NK + +
Sbjct: 61 GLGRE--RVEEARQVADRADLVLLVVDSDLTPVEEEAKLGL-LRERGKPVLLVLNKIDLV 117
Query: 125 NSS------ISLDFYELGIGNPHIISALYGNGIKNFLENILTI 161
S L +SAL G GI + I +
Sbjct: 118 PESEEEELLRERKLELLPDLPVIAVSALPGEGIDELRKKIAEL 160
Score = 103 bits (259), Expect = 2e-25
Identities = 45/167 (26%), Positives = 82/167 (49%), Gaps = 8/167 (4%)
Query: 186 AIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSI-KSLFEYNNKKYILIDTAGIRRRN 244
AI G+PNVGKS+L+N+LLG+N I PGTTRD + K +LIDT G+
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDEE- 59
Query: 245 KTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCVNKWD 304
+ + V + + A++V+L++D+ ++ + E G+ +++ +NK D
Sbjct: 60 ---GGLGRERVEEARQVADRADLVLLVVDSDLTPVEEEAKLGLL-RERGKPVLLVLNKID 115
Query: 305 SIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESINHV 351
+ ++ + + K +L L +SA+ I+ + I +
Sbjct: 116 LVPESEEEELLRERKLEL--LPDLPVIAVSALPGEGIDELRKKIAEL 160
>gnl|CDD|173007 PRK14541, PRK14541, nucleoside diphosphate kinase; Provisional.
Length = 140
Score = 108 bits (271), Expect = 2e-27
Identities = 45/113 (39%), Positives = 74/113 (65%), Gaps = 2/113 (1%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
RT +++ D + K ++G + ++ E+ G +++A +L+K +FY++H+ RPF+ LV
Sbjct: 3 RTLTILKPDCVRKQLIGAVIDKIERAGFRVVAMKKTRLTKETAGEFYAVHRERPFYGELV 62
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAAKGTIRADFAESIDKNIVH 534
FM SGP +LE E+A+ R LIG TDP +AA+GT+R +A+S +NIVH
Sbjct: 63 EFMSSGPCVPMILEKENAVADFRTLIGATDPAEAAEGTVRKLYADSKGENIVH 115
>gnl|CDD|184733 PRK14540, PRK14540, nucleoside diphosphate kinase; Provisional.
Length = 134
Score = 107 bits (269), Expect = 3e-27
Identities = 47/113 (41%), Positives = 71/113 (62%), Gaps = 2/113 (1%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
RTF + DA+E+ ++G+I R+E G +I+ M KL++ E++Y HK + F++ L+
Sbjct: 4 RTFVALKPDAVERKLIGKIIQRFENKGFEIVEMKMLKLTREMAEEYYEEHKGKEFYERLI 63
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAAKGTIRADFAESIDKNIVH 534
NFM SG + V+EGE+AI R +IG T+P +A GTIR DF NI+H
Sbjct: 64 NFMTSGRIVAMVIEGENAISTVRKMIGKTNPAEAEPGTIRGDFGLYTPANIIH 116
>gnl|CDD|226228 COG3705, HisZ, ATP phosphoribosyltransferase involved in histidine
biosynthesis [Amino acid transport and metabolism].
Length = 390
Score = 110 bits (277), Expect = 1e-25
Identities = 79/308 (25%), Positives = 120/308 (38%), Gaps = 44/308 (14%)
Query: 873 IVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMFRHERPQYG 932
+++ ++ DE G L LRP+ T V R P RL Y+G +FR ++G
Sbjct: 57 DLRRRLFKLEDE-TGGRLGLRPDFTIPVARIHATLLA--GTPLRLSYAGKVFRAREGRHG 113
Query: 933 RYRQFYQIGVEAIGFPGPDIDAELIIMCSRLWKNLNLKNICLELNSIGNFN--------- 983
R +F Q G+E +G DAE+I + K L L ++ LEL G F
Sbjct: 114 RRAEFLQAGIELLGDDSAAADAEVIALALAALKALGLADLKLELGHAGIFRALLAAAGLP 173
Query: 984 -----------ERKKYCIDLINYIKKHKDSKWFCEDIKHSLYLNSLRVLDSKNLIIREIL 1032
K + L + S E L +L RE+L
Sbjct: 174 GGWRARLRRAFGDKDL-LGLELLVLAAPLSP---ELRGRLSELLALLG-------GREVL 222
Query: 1033 INAPKLLDYLEKD--SLDHFYGIQKILNYNNISYKINTKLVRGMDYYNRTVFEWTTDKLG 1090
A LLD L +L+ + I ++ +R DYY VF D LG
Sbjct: 223 ERARGLLDELMAQGIALNEGRALADIARRLIEKIALDLGRLRHFDYYTGLVFLAYADGLG 282
Query: 1091 SQNSICGGGRYDFLIKKFSNKFVPASGFAIGIERL----IELIKKININHNFSHQCDIYI 1146
+++ GGRYD L+ F PA+GFA+ ++ L + L ++ F + D Y
Sbjct: 283 --DALASGGRYDGLLGLFGRA-APATGFALRLDALAQGGLPLEERRYAAL-FGRELDYYT 338
Query: 1147 VHVGKEAE 1154
+ A+
Sbjct: 339 GAAFEAAQ 346
>gnl|CDD|178145 PLN02530, PLN02530, histidine-tRNA ligase.
Length = 487
Score = 112 bits (281), Expect = 1e-25
Identities = 103/377 (27%), Positives = 174/377 (46%), Gaps = 48/377 (12%)
Query: 867 SGEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYS-GPMFR 925
+GEE + ++Y+F D+ G ++LRPE T S+ R V++ P + W++ G +R
Sbjct: 121 AGEE---ITDQLYNFEDK-GGRRVALRPELTPSLARLVLQKGKSLSLPLK-WFAIGQCWR 175
Query: 926 HERPQYGRYRQFYQIGVEAIGFPGPDIDAELIIMCSRLWKNLNL--KNICLELNSIGNFN 983
+ER GR R+ YQ ++ IG PG + +AEL+ +K + + ++ ++++S
Sbjct: 176 YERMTRGRRREHYQWNMDIIGVPGVEAEAELLAAIVTFFKRVGITSSDVGIKVSSRKVLQ 235
Query: 984 E-RKKY----------CIDL-------INYIKKHKDSKWFCED-IKHSLYLNSLRVLDSK 1024
K Y C+ + I+K D+ E+ I+ L + SL+ LD
Sbjct: 236 AVLKSYGIPEESFAPVCVIVDKLEKLPREEIEKELDTLGVSEEAIEGILDVLSLKSLDD- 294
Query: 1025 NLIIREILINAPKLLDYLEK-DSLDHFYGIQKILNYNNISYKINTKLVRGMDYYNRTVFE 1083
+ +L + + L++ SL YG Q L ++ +VRG+ YY VFE
Sbjct: 295 ---LEALLGADSEAVADLKQLFSLAEAYGYQDWLVFD-------ASVVRGLAYYTGIVFE 344
Query: 1084 WTTDKLGSQNSICGGGRYDFLIKKFSNKFVPASGFAIGIERLIELIKKININHNFSHQCD 1143
D+ G +ICGGGRYD L+ F + PA GF G ++EL+K+ + HQ D
Sbjct: 345 -GFDRAGKLRAICGGGRYDRLLSTFGGEDTPACGFGFGDAVIVELLKEKGLLPELPHQVD 403
Query: 1144 IYIVHVGKEAELKAFVLSENLRTLGLKVILNCVFNNIHES--FKSQMKRANASNANFAAI 1201
+ + ++ + A ++ LR G V L + E K K A A +
Sbjct: 404 DVVFALDEDLQGAAAGVASRLREKGRSVDL------VLEPKKLKWVFKHAERIGAKRLVL 457
Query: 1202 IGENEIINNTLIIKDLR 1218
+G +E + +KDL
Sbjct: 458 VGASEWERGMVRVKDLS 474
>gnl|CDD|216009 pfam00587, tRNA-synt_2b, tRNA synthetase class II core domain (G,
H, P, S and T). Other tRNA synthetase sub-families are
too dissimilar to be included. This domain is the core
catalytic domain of tRNA synthetases and includes
glycyl, histidyl, prolyl, seryl and threonyl tRNA
synthetases.
Length = 171
Score = 104 bits (262), Expect = 1e-25
Identities = 41/139 (29%), Positives = 63/139 (45%), Gaps = 8/139 (5%)
Query: 867 SGEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIY-DGPKRLWYSGPMFR 925
SG D ++EMY F D G+ L LRP + R L Y + P +L+ GP FR
Sbjct: 35 SGHWDDYFEEEMYKFKDR-GGEELYLRPTAEVGITRLFKNEILSYRELPLKLYQIGPCFR 93
Query: 926 HE-RPQYG--RYRQFYQIGVEAIGFP--GPDIDAELIIMCSRLWKNLNLKNICLELNSIG 980
+E RP+ G R R+F Q+ E G P + EL+ + + ++L L + L + G
Sbjct: 94 YEARPRRGLGRVREFTQVDAEIFGTPEQSEEELEELLKLAEEILQDLGL-PYRVVLATTG 152
Query: 981 NFNERKKYCIDLINYIKKH 999
+ DL ++
Sbjct: 153 DLGGSASKEGDLEAWLPAE 171
>gnl|CDD|173008 PRK14542, PRK14542, nucleoside diphosphate kinase; Provisional.
Length = 137
Score = 101 bits (253), Expect = 5e-25
Identities = 52/113 (46%), Positives = 70/113 (61%), Gaps = 2/113 (1%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
RTF +I D ++ VG I R EK G KI+ KLS D ++FY +H RPF+ +L
Sbjct: 3 RTFIMIKPDGVKNKHVGNILQRIEKEGFKILGLKYLKLSLEDAKQFYKVHSARPFYNDLC 62
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAAKGTIRADFAESIDKNIVH 534
N+M SGP+ LE ++A+ R +IG TDP +AA GTIRA +AES + N VH
Sbjct: 63 NYMSSGPIVAAALERDNAVLHWREVIGATDPKEAAAGTIRALYAESKEANAVH 115
>gnl|CDD|178228 PLN02619, PLN02619, nucleoside-diphosphate kinase.
Length = 238
Score = 102 bits (255), Expect = 4e-24
Identities = 67/202 (33%), Positives = 93/202 (46%), Gaps = 22/202 (10%)
Query: 354 SSIIHLSTSRITRALISAIKNHPPCRKKLIRPKLRYAHQGGKNPPIIVIHGNRLKYIGND 413
SS I S SR R+L+S+ KN + GGK P + G R
Sbjct: 2 SSQICRSASRAARSLLSSAKNASFLSEGRAVAAAAAVSAGGKPPLLASAFG-RATGSSTA 60
Query: 414 YKRYLEKYFY-------------------RTFSLI--DALEKNIVGEIYNRYEKIGLKII 452
+++ RTF I D +++ ++ EI +R+E+ G K++
Sbjct: 61 SAQWISGALALPAAVYMLQEQEAHAAEMERTFIAIKPDGVQRGLISEIISRFERKGFKLV 120
Query: 453 AAYMKKLSKNDVEKFYSIHKNRPFFKNLVNFMISGPVFIQVLEGEDAIKKHRILIGDTDP 512
A + SK +K Y K RPFF L +F+ SGPV V EGE IK R LIG TDP
Sbjct: 121 AIKVVVPSKEFAQKHYHDLKERPFFNGLCDFLSSGPVVAMVWEGEGVIKYGRKLIGATDP 180
Query: 513 IKAAKGTIRADFAESIDKNIVH 534
K+ GTIR D A + +NI+H
Sbjct: 181 QKSEPGTIRGDLAVVVGRNIIH 202
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 102 bits (257), Expect = 1e-23
Identities = 50/172 (29%), Positives = 89/172 (51%), Gaps = 21/172 (12%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRRRN 244
VAIVG+PNVGKSTL+N+L+G+ I P TTR I+ + ++ + I +DT GI +
Sbjct: 8 VAIVGRPNVGKSTLLNALVGQKISIVSPKPQTTRHRIRGIVTEDDAQIIFVDTPGIHKPK 67
Query: 245 KTFEVIEKF---SVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCVN 301
+ + + + +LK + ++V+ ++DA + I D I + + +I+ +N
Sbjct: 68 RA---LNRAMNKAAWSSLK---DVDLVLFVVDADEKIGPGDEFILEKLKKVKTPVILVLN 121
Query: 302 KWDSIIHNQRKIIKNNIKKKLNFLSFAMFNF-----ISAIKLNNINSFMESI 348
K D + K + L LS + +F ISA+K +N++ ++ I
Sbjct: 122 KIDLVKD------KEELLPLLEELS-ELMDFAEIVPISALKGDNVDELLDVI 166
Score = 95.1 bits (238), Expect = 4e-21
Identities = 49/166 (29%), Positives = 80/166 (48%), Gaps = 21/166 (12%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDR-----HYGEGYIGKKSFIIIDTGG-F 60
+VGRPNVGKSTL N L + ++V+ P TR R + I I +DT G
Sbjct: 10 IVGRPNVGKSTLLNALVGQKISIVSPKPQTTRHRIRGIVTEDDAQI-----IFVDTPGIH 64
Query: 61 EPEVKKGIMHE-MTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVIN 119
+P K ++ M K ++ + D+++F+VD + + D+ I L+K P++LV+N
Sbjct: 65 KP---KRALNRAMNKAAWSSLKDVDLVLFVVDADEKIGPGDEFILEKLKKVKTPVILVLN 121
Query: 120 KSENINSSISL----DFYELGIGNPHI--ISALYGNGIKNFLENIL 159
K + + L + + I ISAL G+ + L+ I
Sbjct: 122 KIDLVKDKEELLPLLEELSELMDFAEIVPISALKGDNVDELLDVIA 167
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 98.3 bits (246), Expect = 1e-23
Identities = 53/165 (32%), Positives = 83/165 (50%), Gaps = 19/165 (11%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDR-----HYGEGYIGKKSFIIIDTGG-F 60
++GRPNVGKSTL N L + ++V+ P TR+R + I I +DT G
Sbjct: 8 IIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIYTDDDAQI-----IFVDTPGIH 62
Query: 61 EPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINK 120
+P+ K G M K A+ + D+++F+VD + + E D+ I L+KS P++LV+NK
Sbjct: 63 KPKKKLG--ERMVKAAWSALKDVDLVLFVVDASEWIGEGDEFILELLKKSKTPVILVLNK 120
Query: 121 SENINSSISL----DFYELGIGNPHI--ISALYGNGIKNFLENIL 159
+ + L + + I ISAL G + LE I+
Sbjct: 121 IDLVKDKEDLLPLLEKLKELHPFAEIFPISALKGENVDELLEYIV 165
Score = 97.9 bits (245), Expect = 2e-23
Identities = 48/166 (28%), Positives = 87/166 (52%), Gaps = 7/166 (4%)
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRRR 243
VAI+G+PNVGKSTL+N+L+G+ I P TTR+ I+ ++ ++ + I +DT GI +
Sbjct: 5 FVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIYTDDDAQIIFVDTPGIHKP 64
Query: 244 NKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCVNKW 303
K + V ++ + ++V+ ++DA + I D I + +S +I+ +NK
Sbjct: 65 KKKL---GERMVKAAWSALKDVDLVLFVVDASEWIGEGDEFILELLKKSKTPVILVLNKI 121
Query: 304 DSIIHNQR-KIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESI 348
D + + + +K+ F ISA+K N++ +E I
Sbjct: 122 DLVKDKEDLLPLLEKLKELHPFAEIFP---ISALKGENVDELLEYI 164
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 104 bits (260), Expect = 3e-23
Identities = 64/192 (33%), Positives = 102/192 (53%), Gaps = 9/192 (4%)
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRRR 243
K+AIVG PNVGKS+L+N+LL ++R I D GTTRD ++ FE N L+DTAGIR
Sbjct: 205 KLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGILIKLLDTAGIR-- 262
Query: 244 NKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCVNKW 303
+ + +E+ + K+ K+I +A++VI +LDA Q ++ D I + +S + I+ +NK
Sbjct: 263 -EHADFVERLGIEKSFKAIKQADLVIYVLDASQPLTKDDFLII-DLNKSKKPFILVLNKI 320
Query: 304 DSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKL--NNINSFMESINHVYDSSIIHLST 361
D + N + ++ + LS + + L IN+F D +I S+
Sbjct: 321 D-LKINSLEFFVSSKVLNSSNLSAKQLKIKALVDLLTQKINAFYSKERVELDDYLI--SS 377
Query: 362 SRITRALISAIK 373
+ L AI
Sbjct: 378 WQAMILLEKAIA 389
Score = 79.1 bits (195), Expect = 4e-15
Identities = 51/172 (29%), Positives = 87/172 (50%), Gaps = 7/172 (4%)
Query: 5 LVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGFEPEV 64
L +VG PNVGKS+L N L A+V++ G TRD G+ + ++DT G E
Sbjct: 206 LAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGILIKLLDTAGIR-EH 264
Query: 65 KKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSENI 124
+ +++ +AI ++D++I+++D Q L + D LI L KS +P +LV+NK +
Sbjct: 265 ADFVERLGIEKSFKAIKQADLVIYVLDASQPLTKDDFLII-DLNKSKKPFILVLNKIDLK 323
Query: 125 NSSISLDFYELGIGNPHIISALYGNGIKNFLENILTIELPYKKFFKKKEFTN 176
+ SL+F+ + IK L ++LT ++ F+ K+
Sbjct: 324 IN--SLEFFVSSKVLNSSNLSAKQLKIKA-LVDLLTQKI--NAFYSKERVEL 370
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 96.7 bits (241), Expect = 5e-23
Identities = 54/162 (33%), Positives = 79/162 (48%), Gaps = 11/162 (6%)
Query: 182 YIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKY--ILIDTAG 239
IK+ IVG PNVGKSTL+N LLG IT PGTTR+ + ++ E + K Y L+DTAG
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
Query: 240 IRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVC 299
+ I + S+ ++VIL+LD ++ + Q I + ESG +I+
Sbjct: 61 QEDYDA----IRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHA-ESGVPIILV 115
Query: 300 VNKWDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNI 341
NK D +K ++ L+ +SA NI
Sbjct: 116 GNKIDLRDAK----LKTHVAFLFAKLNGEPIIPLSAETGKNI 153
Score = 76.6 bits (189), Expect = 4e-16
Identities = 51/158 (32%), Positives = 78/158 (49%), Gaps = 15/158 (9%)
Query: 3 PVLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYI----GKKSFIIIDTG 58
+V+VG PNVGKSTL NRL ++ ++ PG T R+Y I F ++DT
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTT--RNYVTTVIEEDGKTYKFNLLDTA 59
Query: 59 GFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVI 118
G E I + + ++ DI+I ++D + L +Q K I + +SG PI+LV
Sbjct: 60 GQED--YDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIH-HAESGVPIILVG 116
Query: 119 NKSENINSSIS----LDFYELGIGNPHI-ISALYGNGI 151
NK + ++ + F +L G P I +SA G I
Sbjct: 117 NKIDLRDAKLKTHVAFLFAKLN-GEPIIPLSAETGKNI 153
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 99 bits (250), Expect = 7e-23
Identities = 54/184 (29%), Positives = 90/184 (48%), Gaps = 10/184 (5%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGF-EPEVK 65
++GRPNVGKSTL N L + ++V+ P TR+R G I +DT G +P K
Sbjct: 11 IIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIFVDTPGIHKP--K 68
Query: 66 KGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSENIN 125
+ M K + A+ + D+I+F+VD +G D+ I L+K+ P++LV+NK + +
Sbjct: 69 HALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLKKTKTPVILVVNKIDKVK 128
Query: 126 SSISL----DFYELGIGNPHI--ISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIHS 179
L F + + I ISAL G+ + L I+ LP ++ ++
Sbjct: 129 PKTVLLKLIAFLKKLLPFKEIVPISALKGDNVD-TLLEIIKEYLPEGPWYYPEDQITDRP 187
Query: 180 IEYI 183
++
Sbjct: 188 ERFL 191
Score = 99.2 bits (248), Expect = 2e-22
Identities = 51/171 (29%), Positives = 94/171 (54%), Gaps = 11/171 (6%)
Query: 181 EYIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGI 240
+ VAI+G+PNVGKSTL+N+L+G+ I P TTR+ I+ + +N + I +DT GI
Sbjct: 5 KSGFVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIFVDTPGI 64
Query: 241 -RRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVC 299
+ ++ E++ K + LK + ++++ ++DA + D I + ++ +I+
Sbjct: 65 HKPKHALGELMNK-AARSALK---DVDLILFVVDADEGWGPGDEFILEQLKKTKTPVILV 120
Query: 300 VNKWDSIIHNQRKI--IKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESI 348
VNK D + + + + +KK L F ISA+K +N+++ +E I
Sbjct: 121 VNKIDK-VKPKTVLLKLIAFLKKLLPFKEIVP---ISALKGDNVDTLLEII 167
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 91.3 bits (227), Expect = 5e-20
Identities = 57/182 (31%), Positives = 88/182 (48%), Gaps = 8/182 (4%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGFEPEVKK 66
++GRPNVGKSTL N+L + ++ + TR+R G G I IDT GF E K
Sbjct: 5 ILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFIDTPGFH-EKKH 63
Query: 67 GIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSENINS 126
+ M K+ + AI D+I+F+VD Q + + ++T L+ +P+VL NK +N
Sbjct: 64 SLNRLMMKEARSAIGGVDLILFVVDSDQWNGDGEFVLTK-LQNLKRPVVLTRNKLDNKFK 122
Query: 127 SISL---DFYELGIGNPHI--ISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIHSIE 181
L D Y + I ISAL G+ +FL + + LP F +++
Sbjct: 123 DKLLPLIDKYAILEDFKDIVPISALTGDNT-SFLAAFIEVHLPEGPFRYPEDYVTDQPDR 181
Query: 182 YI 183
+
Sbjct: 182 FK 183
Score = 79.7 bits (197), Expect = 4e-16
Identities = 36/165 (21%), Positives = 76/165 (46%), Gaps = 6/165 (3%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGI-R 241
VAI+G+PNVGKSTL+N L G+ IT TTR+ I + + I IDT G
Sbjct: 1 GFVAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFIDTPGFHE 60
Query: 242 RRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCVN 301
+++ ++ K + + ++++ ++D+ Q + + + R +++ N
Sbjct: 61 KKHSLNRLMMK-EARSAIGGV---DLILFVVDSDQW-NGDGEFVLTKLQNLKRPVVLTRN 115
Query: 302 KWDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFME 346
K D+ ++ + + +F + ++ + + +F+E
Sbjct: 116 KLDNKFKDKLLPLIDKYAILEDFKDIVPISALTGDNTSFLAAFIE 160
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 87.9 bits (218), Expect = 5e-20
Identities = 47/165 (28%), Positives = 70/165 (42%), Gaps = 14/165 (8%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYI--GKKSFIIIDTGGFEPE 63
V+VGR VGKS+L N L V++ PG TRD + GK +++DT G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 64 VKKGIMHEMTKQTKQAIIESDIIIFIVDG--RQGLVEQDKLITNFLRKSGQPIVLVINKS 121
G + + +D+I+ +VD R+ + LI LRK G PI+LV NK
Sbjct: 61 GGLGREEL----ARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNKI 116
Query: 122 ----ENINSSISLDFYELGIGNPHII--SALYGNGIKNFLENILT 160
E + I + SA G G+ E ++
Sbjct: 117 DLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
Score = 87.1 bits (216), Expect = 1e-19
Identities = 38/167 (22%), Positives = 72/167 (43%), Gaps = 12/167 (7%)
Query: 186 AIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYI--LIDTAGIRRR 243
+VG+ VGKS+L+N+LLG D PGTTRD + E + K L+DT G+
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 244 NKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDI--NIANFIYESGRSLIVCVN 301
+++ A++++L++D+ S +D I + + G +I+ N
Sbjct: 61 GGLGREELARLLLR------GADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGN 114
Query: 302 KWDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESI 348
K D + + + + + + +SA ++ E +
Sbjct: 115 KIDLLEEREVEELLRLEELA--KILGVPVFEVSAKTGEGVDELFEKL 159
>gnl|CDD|173010 PRK14544, PRK14544, nucleoside diphosphate kinase; Provisional.
Length = 183
Score = 84.9 bits (210), Expect = 1e-18
Identities = 46/148 (31%), Positives = 70/148 (47%), Gaps = 43/148 (29%)
Query: 430 DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFY--------------------- 468
DA+++ +VGEI +R+EK GLKI+A M K + +E+FY
Sbjct: 13 DAVKRGLVGEIISRFEKAGLKIVAMKMVKATPEQIERFYPSSEEWYRSVGNKLLKAYQEL 72
Query: 469 ------------SIHKNRPFFKNLVNFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAA 516
+ + ++LV +M SGP+ VL+G A++ R L+G T P KA
Sbjct: 73 GIDPRARLGTDDPVEVGKKVKESLVKYMTSGPIVAMVLKGNRAVEVVRKLVGPTSPHKAP 132
Query: 517 KGTIRADFA-ESID---------KNIVH 534
GTIR D++ +S D N+VH
Sbjct: 133 PGTIRGDYSIDSPDLAAEEGRVVYNLVH 160
>gnl|CDD|239878 cd04415, NDPk7A, Nucleoside diphosphate kinase 7 domain A (NDPk7A):
The nm23-H7 class of nucleoside diphosphate kinase
(NDPk7) consists of an N-terminal DM10 domain and two
functional catalytic NDPk modules, NDPk7A and NDPk7B.
The function of the DM10 domain, which also occurs in
multiple copies in other proteins, is unknown. NDPk7 is
predominantly expressed in testes, although appreciable
amount are also found in liver, heart, brain, ovary,
small intestine and spleen. The nm23-H7 gene is located
in or near the hereditary prostrate cancer
susceptibility locus. Nm23-H7 may be involved in the
development of colon and gastric carcinoma, the latter
possibly in a type-specific manner.
Length = 131
Score = 82.1 bits (203), Expect = 2e-18
Identities = 45/116 (38%), Positives = 64/116 (55%), Gaps = 7/116 (6%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
+T +LI DA K +G+I E G I A M KLS+ + + FY+ H+++PF+ LV
Sbjct: 2 KTLALIKPDAYSK--IGKIIQIIEDAGFTITKAKMTKLSRKEAQDFYAEHQSKPFYNELV 59
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKA---AKGTIRADFAESIDKNIVH 534
FM SGP+ L G+DAI + R L+G T+ A A +IRA F +N H
Sbjct: 60 QFMTSGPIVAMELVGDDAISEWRKLLGPTNSSVARSDAPNSIRALFGTDGTRNAAH 115
>gnl|CDD|237097 PRK12420, PRK12420, histidyl-tRNA synthetase; Provisional.
Length = 423
Score = 88.2 bits (219), Expect = 4e-18
Identities = 95/396 (23%), Positives = 160/396 (40%), Gaps = 62/396 (15%)
Query: 868 GEETDIVKKEMYSFIDELNGD-NLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMFRH 926
G+E + KE+Y+ D+ G +L+LR + T + V N I KR + G +FR
Sbjct: 58 GDE---ILKEIYTLTDQ--GKRDLALRYDLTIPFAKVVAMNPNIRLPFKR-YEIGKVFRD 111
Query: 927 ERPQYGRYRQFYQIGVEAIGFPGPDIDAELIIMCSRLWKNLNLKNICLELNS-------I 979
+ GR+R+F Q V+ +G +AEL+ M L++ LNL + ++ N+ +
Sbjct: 112 GPIKQGRFREFIQCDVDIVGVESVMAEAELMSMAFELFRRLNL-EVTIQYNNRKLLNGIL 170
Query: 980 GNFNERKKYCIDLINYIKKHKDSKWFCEDIKHSLYLNSLRVLDSKNLIIREILINAPKLL 1039
+ D+I + K E I L + I +
Sbjct: 171 QAIGIPTELTSDVILSLDK-------IEKIGIDGVRKDLLERGISEEMADTIC----NTV 219
Query: 1040 DYLEKDSLDHFYGI----------------QKILNYNNIS--YKINTKLVRGMDYYNRTV 1081
+ S+ F Q+ L I+ N L RG+ Y TV
Sbjct: 220 LSCLQLSIADFKEAFNNPLVAEGVNELQQLQQYLIALGINENCIFNPFLARGLTMYTGTV 279
Query: 1082 FEWTTDKLGS-QNSICGGGRYDFLIKKF--SNKFVPASGFAIGIERLIELIKKININHNF 1138
+E K GS +SI GGRYD +I F + P G + G++ + + +
Sbjct: 280 YE-IFLKDGSITSSIGSGGRYDNIIGAFRGDDMNYPTVGISFGLDVIYTALSQKET---I 335
Query: 1139 SHQCDIYIVHVGKEAELKAFVLSENLR-TLGLKVILNCVFNNIHESFKSQMKRANASNAN 1197
S D++I+ +G E + +++ LR T GLKV L K + AN N
Sbjct: 336 SSTADVFIIPLGTELQ--CLQIAQQLRSTTGLKVELELA----GRKLKKALNYANKENIP 389
Query: 1198 FAAIIGENEIINNTLIIKDLRNKYEDPTLKQISISF 1233
+ IIGE E+ T+++++++ E + +S
Sbjct: 390 YVLIIGEEEVSTGTVMLRNMKEGSEVK----VPLSS 421
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 86.8 bits (216), Expect = 7e-18
Identities = 51/167 (30%), Positives = 84/167 (50%), Gaps = 20/167 (11%)
Query: 5 LVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSF--------IIID 56
+ + GR N GKS+L N LT A+V++ PG T D Y K+ ++ID
Sbjct: 9 IGIFGRRNAGKSSLINALTGQDIAIVSDVPGTTTDPVY-------KAMELLPLGPVVLID 61
Query: 57 TGGFEPEVKKGIMHEM-TKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIV 115
T G + E + G E+ ++T++ + ++D+ + +VD G E + + L++ P +
Sbjct: 62 TAGLDDEGELG---ELRVEKTREVLDKTDLALLVVDAGVGPGEYELELIEELKERKIPYI 118
Query: 116 LVINKSENINSSISLDFYELGIGNPHI-ISALYGNGIKNFLENILTI 161
+VINK + S L+ E G P I +SAL G GI E I+ +
Sbjct: 119 VVINKIDLGEESAELEKLEKKFGLPPIFVSALTGEGIDELKEAIIEL 165
Score = 78.7 bits (195), Expect = 3e-15
Identities = 48/179 (26%), Positives = 75/179 (41%), Gaps = 40/179 (22%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYIL-------IDT 237
+ I G+ N GKS+LIN+L G++ I D PGTT D + E +L IDT
Sbjct: 9 IGIFGRRNAGKSSLINALTGQDIAIVSDVPGTTTDPVYKAME------LLPLGPVVLIDT 62
Query: 238 AGI--------RRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFI 289
AG+ R KT EV++K ++ +L++DA ++ + +
Sbjct: 63 AGLDDEGELGELRVEKTREVLDK------------TDLALLVVDAGVGPGEYELELIEEL 110
Query: 290 YESGRSLIVCVNKWDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESI 348
E IV +NK D + K L + F+SA+ I+ E+I
Sbjct: 111 KERKIPYIVVINKIDLGEESAELEKLEK-KFGLPPI------FVSALTGEGIDELKEAI 162
>gnl|CDD|238359 cd00670, Gly_His_Pro_Ser_Thr_tRS_core, Gly_His_Pro_Ser_Thr_tRNA
synthetase class II core domain. This domain is the core
catalytic domain of tRNA synthetases of the subgroup
containing glycyl, histidyl, prolyl, seryl and threonyl
tRNA synthetases. It is primarily responsible for
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. These enzymes belong to class II
aminoacyl-tRNA synthetases (aaRS) based upon their
structure and the presence of three characteristic
sequence motifs in the core domain. This domain is also
found at the C-terminus of eukaryotic GCN2 protein
kinase and at the N-terminus of the ATP
phosphoribosyltransferase accessory subunit, HisZ and
the accessory subunit of mitochondrial polymerase gamma
(Pol gamma b) . Most class II tRNA synthetases are
dimers, with this subgroup consisting of mostly
homodimers. These enzymes attach a specific amino acid
to the 3' OH group of ribose of the appropriate tRNA.
Length = 235
Score = 83.6 bits (207), Expect = 1e-17
Identities = 35/126 (27%), Positives = 50/126 (39%), Gaps = 10/126 (7%)
Query: 871 TDIVKKEMYSFID---ELNGDNLSLRPEGTASVIRSVIENNLIY-DGPKRLWYSGPMFRH 926
D +KEMY+F D EL +L LRP + + L Y P RL GP FRH
Sbjct: 41 LDGYRKEMYTFEDKGRELRDTDLVLRPAACEPIYQIFSGEILSYRALPLRLDQIGPCFRH 100
Query: 927 ERPQY---GRYRQFYQIGVEAIGFPG--PDIDAELIIMCSRLWKNLNLKNICLELNSIGN 981
E R R+F Q+ G P + E + + + + L L + + +
Sbjct: 101 EPSGRRGLMRVREFRQVEYVVFGEPEEAEEERREWLELAEEIARELGL-PVRVVVADDPF 159
Query: 982 FNERKK 987
F K
Sbjct: 160 FGRGGK 165
Score = 31.2 bits (71), Expect = 2.7
Identities = 16/66 (24%), Positives = 21/66 (31%), Gaps = 11/66 (16%)
Query: 1072 RGMDYYNRTVFEWTTDKL--GSQNSICGGGRY--------DFLIKKFSN-KFVPASGFAI 1120
RG+D TV E+ G G F I + + G A
Sbjct: 166 RGLDAGRETVVEFELLLPLPGRAKETAVGSANVHLDHFGASFKIDEDGGGRAHTGCGGAG 225
Query: 1121 GIERLI 1126
G ERL+
Sbjct: 226 GEERLV 231
>gnl|CDD|238436 cd00859, HisRS_anticodon, HisRS Histidyl-anticodon binding domain.
HisRS belongs to class II aminoacyl-tRNA synthetases
(aaRS). This alignment contains the anticodon binding
domain, which is responsible for specificity in
tRNA-binding, so that the activated amino acid is
transferred to a ribose 3' OH group of the appropriate
tRNA only.
Length = 91
Score = 78.7 bits (195), Expect = 1e-17
Identities = 28/100 (28%), Positives = 49/100 (49%), Gaps = 10/100 (10%)
Query: 1141 QCDIYIVHVGKEAELKAFVLSENLRTLGLKVILNCVFNNIHESFKSQMKRANASNANFAA 1200
+ D+Y+V +G+ A +A L+E LR G+K ++ K Q K A+ S A FA
Sbjct: 1 EVDVYVVPLGEGALSEALELAEQLRDAGIKAEIDY----GGRKLKKQFKYADRSGARFAV 56
Query: 1201 IIGENEIINNTLIIKDLRNKYEDPTLKQISISFKDAENYF 1240
I+GE+E+ + +KDL +Q +++ +
Sbjct: 57 ILGEDELAAGVVTVKDLETG------EQETVALDELVEEL 90
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 77.9 bits (193), Expect = 1e-16
Identities = 53/167 (31%), Positives = 81/167 (48%), Gaps = 28/167 (16%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDT------GGF 60
LVG PNVGK+TLFN LT +R V N+PG+T ++ GE +G K I+D +
Sbjct: 2 LVGNPNVGKTTLFNALTGAR-QKVGNWPGVTVEKKEGEFKLGGKEIEIVDLPGTYSLTPY 60
Query: 61 EPEVKKGIMHEMTKQTKQAII--ESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVI 118
+ E K + ++ E D+I+ +VD +E++ +T L + G P+V+ +
Sbjct: 61 SED-------E--KVARDFLLGEEPDLIVNVVDATN--LERNLYLTLQLLELGLPVVVAL 109
Query: 119 NKS-ENINSSISLDF----YELGIGNPHI-ISALYGNGIKNFLENIL 159
N E I +D LG+ P + SA G GI L+ I
Sbjct: 110 NMIDEAEKRGIKIDLDKLSELLGV--PVVPTSARKGEGIDELLDAIA 154
Score = 53.2 bits (129), Expect = 6e-08
Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 186 AIVGKPNVGKSTLINSLLGEN-RVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGI 240
A+VG PNVGK+TL N+L G +V + PG T + + F+ K+ ++D G
Sbjct: 1 ALVGNPNVGKTTLFNALTGARQKVGNW--PGVTVEKKEGEFKLGGKEIEIVDLPGT 54
>gnl|CDD|215503 PLN02931, PLN02931, nucleoside diphosphate kinase family protein.
Length = 177
Score = 78.3 bits (193), Expect = 2e-16
Identities = 43/116 (37%), Positives = 59/116 (50%), Gaps = 5/116 (4%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
RT ++I D L N I + G I+ +L ++ FY+ H +R FF +LV
Sbjct: 31 RTLAMIKPDGLSGNYTERIKEVILESGFSIVKEMTTQLDEDRASLFYAEHSSRSFFPSLV 90
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAA---KGTIRADFAESIDKNIVH 534
+M SGPV + VLE E+A+ R LIG TD KA +IRA +KN VH
Sbjct: 91 KYMTSGPVLVMVLEKENAVSDWRTLIGPTDARKAKISHPNSIRAMCGLDSEKNCVH 146
>gnl|CDD|237749 PRK14543, PRK14543, nucleoside diphosphate kinase; Provisional.
Length = 169
Score = 77.6 bits (191), Expect = 2e-16
Identities = 37/109 (33%), Positives = 66/109 (60%), Gaps = 7/109 (6%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFY-----SIHKNRPF 476
+T +I D + + ++G + +R+E++GLKI+AA M + ++ EK Y ++
Sbjct: 7 KTLCIIKPDGVRRGLIGNVVSRFERVGLKIVAAKMLLVDRSMAEKHYLYDDIAVRHGEAV 66
Query: 477 FKNLVNFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAAKGTIRADFA 525
+K+L+ F+ S PVF+ V+EG ++++ R G T+P A GTIR DF+
Sbjct: 67 WKSLIKFISSSPVFVFVVEGVESVEVVRKFCGSTEPKLAIPGTIRGDFS 115
>gnl|CDD|239879 cd04416, NDPk_TX, NDP kinase domain of thioredoxin
domain-containing proteins (TXNDC3 and TXNDC6): Txl-2
(TXNDC6) and Sptrx-2 (TXNDC3) are fusion proteins of
Group II N-terminal thioredoxin domains followed by one
or three NDP kinase domains, respectively. Sptrx-2,
which has a tissue specific distribution in human
testis, has been considered as a member of the nm23
family (nm23-H8) and exhibits a high homology with sea
urchin IC1 (intermediate chain-1) protein, a component
of the sperm axonemal outer dynein arm complex. Txl-2 is
mainly represented in close association with
microtubules within tissues with cilia and flagella such
as seminiferous epithelium (spermatids) and lung airway
epithelium, suggesting possible role in control of
microtubule stability and maintenance.
Length = 132
Score = 74.9 bits (185), Expect = 8e-16
Identities = 41/116 (35%), Positives = 65/116 (56%), Gaps = 6/116 (5%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
T +LI DA+ + EI + ++ G +I+A L++ +FY H+ +F++LV
Sbjct: 2 YTLALIKPDAVAEK-KDEILEKIKEAGFEILAQKEMVLTEEQAREFYKEHEEEDYFEDLV 60
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAAK---GTIRADFAESIDKNIVH 534
FM SGP I VL E+A+++ R L+G TDP +A + ++RA FA N VH
Sbjct: 61 EFMTSGPSLILVLSKENAVEEWRELMGPTDPEEAKEEKPDSLRAQFARDHLSNAVH 116
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 73.7 bits (182), Expect = 5e-15
Identities = 46/176 (26%), Positives = 82/176 (46%), Gaps = 19/176 (10%)
Query: 185 VAIVGKPNVGKSTLINSLLGENR-VITYDTPGTTRDSIKSLFEYN-NKKYILIDTAG--- 239
VA G+ NVGKS+LIN+L + T TPG T+ + +N K+ L+D G
Sbjct: 2 VAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQ----LINFFNVGDKFRLVDLPGYGY 57
Query: 240 ----IRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRS 295
R K ++IE++ ++ +++ V+LL+DA+ + D+ + F+ E G
Sbjct: 58 AKVSKEVREKWGKLIEEY--LENRENL---KGVVLLIDARHGPTPIDLEMLEFLEELGIP 112
Query: 296 LIVCVNKWDSIIHNQRKIIKNNIKKKLN-FLSFAMFNFISAIKLNNINSFMESINH 350
++ + K D + ++ + IK++LN F S+ K I+ I
Sbjct: 113 FLIVLTKADKLKKSELAKVLKKIKEELNLFNILPPVILFSSKKGTGIDELRALIAE 168
Score = 63.3 bits (155), Expect = 3e-11
Identities = 40/172 (23%), Positives = 74/172 (43%), Gaps = 25/172 (14%)
Query: 6 VLVGRPNVGKSTLFNRLTNS-RDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGF---- 60
GR NVGKS+L N LTN + A + PG T+ ++ + F ++D G+
Sbjct: 3 AFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINF---FNVGDKFRLVDLPGYGYAK 59
Query: 61 -EPEVKKGIMHEMTKQ---TKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVL 116
EV++ ++ ++ ++ + ++ ++D R G D + FL + G P ++
Sbjct: 60 VSKEVRE-KWGKLIEEYLENRENL---KGVVLLIDARHGPTPIDLEMLEFLEELGIPFLI 115
Query: 117 VINKSENINSS-------ISLDFYELGIGNPHII--SALYGNGIKNFLENIL 159
V+ K++ + S + L P +I S+ G GI I
Sbjct: 116 VLTKADKLKKSELAKVLKKIKEELNLFNILPPVILFSSKKGTGIDELRALIA 167
>gnl|CDD|239877 cd04414, NDPk6, Nucleoside diphosphate kinase 6 (NDP kinase 6,
NDPk6, NM23-H6; NME6; Inhibitor of p53-induced
apoptosis-alpha, IPIA-alpha): The nm23-H6 gene encoding
NDPk6 is expressed mainly in mitochondria, but also
found at a lower level in most tissues. NDPk6 has all
nine residues considered crucial for enzyme structure
and activity, and has been found to have NDP kinase
activity. It may play a role in cell growth and cell
cycle progression. The nm23-H6 gene locus has been
implicated in a variety of malignant tumors.
Length = 135
Score = 72.4 bits (178), Expect = 7e-15
Identities = 36/116 (31%), Positives = 57/116 (49%), Gaps = 6/116 (5%)
Query: 425 TFSLI--DALEKN-IVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
T +LI DA+ + + G I+ + + D E+FY+ HK + F+ LV
Sbjct: 3 TLALIKPDAVAHPLALEAVRQLILSNGFTIVRKKELRWTTEDAERFYAEHKGKFFYDRLV 62
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKA---AKGTIRADFAESIDKNIVH 534
+FM SGP + +L E+AIK R L+G T +A A +IR + + +N H
Sbjct: 63 SFMTSGPSWALILAHENAIKTWRALMGPTKVFRARASAPDSIRGLYGLTDTRNATH 118
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 72.9 bits (180), Expect = 2e-14
Identities = 54/191 (28%), Positives = 83/191 (43%), Gaps = 35/191 (18%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGG------ 59
LVG PNVGK+TLFN LT +R V N+PG+T ++ G I+D G
Sbjct: 4 ALVGNPNVGKTTLFNALTGARQH-VGNWPGVTVEKKEGTFKYKGYEIEIVDLPGTYSLSP 62
Query: 60 FEPEVKKGIMHEMTKQTKQAIIES--DIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLV 117
+ E K + + ++E D+II +VD +E++ +T L + G P+V+
Sbjct: 63 YSEEEK--V-------ARDYLLEEKPDVIINVVDATN--LERNLYLTLQLLELGIPVVVA 111
Query: 118 INKS-ENINSSISLDF----YELGIGNPHI-ISALYGNGIKNFLENILTIELPYKKFFKK 171
+N E I +D LG+ P + SA G GI + I+ + +
Sbjct: 112 LNMMDEAEKKGIKIDIKKLSELLGV--PVVPTSARKGEGIDELKDAII-------EVAEG 162
Query: 172 KEFTNIHSIEY 182
K I Y
Sbjct: 163 KVPPAPLRINY 173
Score = 54.8 bits (133), Expect = 3e-08
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGEN-RVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGI 240
I +A+VG PNVGK+TL N+L G V + PG T + + F+Y + ++D G
Sbjct: 1 ITIALVGNPNVGKTTLFNALTGARQHVGNW--PGVTVEKKEGTFKYKGYEIEIVDLPGT 57
>gnl|CDD|215525 PLN02972, PLN02972, Histidyl-tRNA synthetase.
Length = 763
Score = 77.6 bits (191), Expect = 2e-14
Identities = 88/383 (22%), Positives = 158/383 (41%), Gaps = 45/383 (11%)
Query: 868 GEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMFRHE 927
GE++ ++ Y D+ G+ SLR + T R V N + + + ++R +
Sbjct: 379 GEDSKLI----YDLADQ-GGELCSLRYDLTVPFARYVAMNGI---TSFKRYQIAKVYRRD 430
Query: 928 RPQYGRYRQFYQIGVEAIGFPGP-DIDAELIIMCSRLWKNLNLKNICLELNSIGNFNERK 986
P GRYR+FYQ + G P D E+I + + L L++ ++LN +
Sbjct: 431 NPSKGRYREFYQCDFDIAGVYEPMGPDFEIIKVLTELLDELDIGTYEVKLNHRKLLDGML 490
Query: 987 KYC-------------IDLIN-----YIKKHK-DSKWFCEDIKHSLYLNSLRVLDSKNL- 1026
+ C ID ++ +KK + K + + + L
Sbjct: 491 EICGVPPEKFRTICSSIDKLDKQSFEQVKKEMVEEKGLSNETADKI--GNFVKERGPPLE 548
Query: 1027 IIREILINAPKLLD-YLEKDSLDHFYGIQKILNYNNISYKI--NTKLVRGMDYYNRTVFE 1083
++ ++ + L + +LD + K L + KI + L RG+DYY ++E
Sbjct: 549 LLSKLRQEGSEFLGNASSRAALDELEIMFKALEKSKAIGKIVFDLSLARGLDYYTGVIYE 608
Query: 1084 WTTDKLGSQ-NSICGGGRYDFLIKKFSNKFVPASGFAIGIERLIELIKKININHNF---S 1139
G+Q SI GGRYD L+ FS K VPA G ++GIER+ ++++ +
Sbjct: 609 AVF--KGAQVGSIAAGGRYDNLVGMFSGKQVPAVGVSLGIERVFAIMEQQEEEKSQVIRP 666
Query: 1140 HQCDIYIVHVGKEAELKAFVLSENLRTLGLKVILNCVFNNIHESFKSQMKRANASNANFA 1199
+ ++ + +G + A L L G+K + +KRA S +
Sbjct: 667 TETEVLVSIIGDDKLALAAELVSELWNAGIKAEY-----KVSTRKAKHLKRAKESGIPWM 721
Query: 1200 AIIGENEIINNTLIIKDLRNKYE 1222
++GE E+ + +K+L E
Sbjct: 722 VLVGEKELSKGFVKLKNLEAGVE 744
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 70.2 bits (173), Expect = 8e-14
Identities = 45/178 (25%), Positives = 76/178 (42%), Gaps = 19/178 (10%)
Query: 69 MHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKS----ENI 124
M + +Q K+ + D++I + D R L ++ + L +P ++V+NK+
Sbjct: 6 MAKALRQIKEKLKLVDVVIEVRDARIPLSSRNPDLDKILGN--KPRLIVLNKADLADPAK 63
Query: 125 NSSISLDFYELGIGNPHIISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIHSIEYIK 184
L +++ ++A G G+K L+ + +K K ++
Sbjct: 64 TKKW-LKYFKSQGEPVLFVNAKNGKGVKKLLKKAKKLLKENEKLKAKGLLPRP-----LR 117
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDS--IKSLFEYNNKKYILIDTAGI 240
+VG PNVGKSTLIN L G+ + PG TR I+ L+DT GI
Sbjct: 118 AMVVGIPNVGKSTLINRLRGKKVAKVGNKPGVTRGQQWIRI-----GPNIELLDTPGI 170
Score = 49.4 bits (119), Expect = 1e-06
Identities = 21/39 (53%), Positives = 26/39 (66%), Gaps = 1/39 (2%)
Query: 1 MKPVLVLV-GRPNVGKSTLFNRLTNSRDALVANYPGLTR 38
+P+ +V G PNVGKSTL NRL + A V N PG+TR
Sbjct: 113 PRPLRAMVVGIPNVGKSTLINRLRGKKVAKVGNKPGVTR 151
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 74.6 bits (184), Expect = 2e-13
Identities = 48/173 (27%), Positives = 78/173 (45%), Gaps = 28/173 (16%)
Query: 1 MKPVLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGF 60
K + LVG PNVGK+TLFN LT + V N+PG+T ++ G+ I+D G
Sbjct: 2 KKLTVALVGNPNVGKTTLFNALTGAN-QKVGNWPGVTVEKKEGKLKYKGHEIEIVDLPG- 59
Query: 61 EPEVKKGIMHEMT------KQTKQAIIES--DIIIFIVDGRQGLVEQDKLITNFLRKSGQ 112
+ +T K + ++E D+I+ +VD +E++ +T L + G
Sbjct: 60 --------TYSLTAYSEDEKVARDFLLEGKPDLIVNVVDATN--LERNLYLTLQLLELGI 109
Query: 113 PIVLVIN-----KSENINSSISLDFYELGIGNPHI-ISALYGNGIKNFLENIL 159
P++L +N K I I LG+ P + A G G++ I+
Sbjct: 110 PMILALNMIDEAKKRGIRIDIEKLSKLLGV--PVVPTVAKRGEGLEELKRAII 160
Score = 60.4 bits (147), Expect = 5e-09
Identities = 41/186 (22%), Positives = 80/186 (43%), Gaps = 26/186 (13%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGEN-RVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIR 241
+ VA+VG PNVGK+TL N+L G N +V + PG T + + +Y + ++D G
Sbjct: 4 LTVALVGNPNVGKTTLFNALTGANQKVGNW--PGVTVEKKEGKLKYKGHEIEIVDLPGTY 61
Query: 242 RRNKTFEVIEKFSVIKTLKSILE--ANVVILLLDAQQ-----NISAQDINIANFIYESGR 294
+ EK + +LE ++++ ++DA ++ Q + E G
Sbjct: 62 SLT-AYSEDEKVAR----DFLLEGKPDLIVNVVDATNLERNLYLTLQ-------LLELGI 109
Query: 295 SLIVCVNKWDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESINHVYDS 354
+I+ +N D +++ I+ +I+K L + A + + +I + +S
Sbjct: 110 PMILALNMID---EAKKRGIRIDIEKLSKLLGVPVV-PTVAKRGEGLEELKRAIIELAES 165
Query: 355 SIIHLS 360
Sbjct: 166 KTTPRE 171
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 71.9 bits (177), Expect = 6e-13
Identities = 59/205 (28%), Positives = 87/205 (42%), Gaps = 34/205 (16%)
Query: 3 PVLVLVGRPNVGKSTLFNRLTN----SRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTG 58
P++ LVG N GKSTLFN LT D L A TR G+G + ++ DT
Sbjct: 193 PLVALVGYTNAGKSTLFNALTGADVYVADQLFATLDPTTRRIELGDG----RKVLLTDTV 248
Query: 59 GFEPEVKKGIMHEMT---KQTKQAIIESDIIIFIVDGRQGLVEQDKLITNF-----LRKS 110
GF + + H + K T + + E+D+++ +VD + + KL +
Sbjct: 249 GF----IRDLPHPLVEAFKSTLEEVKEADLLLHVVDASDPEILE-KLEAVEDVLAEIGAD 303
Query: 111 GQPIVLVINKSENINSSISLDFYELGIGNPHIISALYGNGIKNFLENI----------LT 160
PI+LV+NK + + L E G NP ISA G G+ E I +T
Sbjct: 304 EIPIILVLNKIDLLEDEEILAELERGSPNPVFISAKTGEGLDLLRERIIELLSGLRTEVT 363
Query: 161 IELPYKK---FFKKKEFTNIHSIEY 182
+ELPY + + EY
Sbjct: 364 LELPYTDAGRLSWLHDNGIVLEEEY 388
Score = 44.2 bits (105), Expect = 4e-04
Identities = 44/172 (25%), Positives = 73/172 (42%), Gaps = 39/172 (22%)
Query: 151 IKNFLENILTIELPYKKFFKKKEFTNIHSIEYIKVAIVGKPNVGKSTLINSLLGENRVI- 209
+K LEN+ P +K + VA+VG N GKSTL N+L G + +
Sbjct: 169 LKRELENVEKAREPRRKKRSRSGIP--------LVALVGYTNAGKSTLFNALTGADVYVA 220
Query: 210 -----TYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRRRNKTFEVIEKFSVIKTLKSILE 264
T D TTR + + +K +L DT G R ++E F TL+ + E
Sbjct: 221 DQLFATLDP--TTR----RIELGDGRKVLLTDTVGFIRDLPH-PLVEAFKS--TLEEVKE 271
Query: 265 ANVVILLLDA-----QQNISA-----QDINIANFIYESGRSLIVCVNKWDSI 306
A++++ ++DA + + A +I +I+ +NK D +
Sbjct: 272 ADLLLHVVDASDPEILEKLEAVEDVLAEIGA------DEIPIILVLNKIDLL 317
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 70.5 bits (173), Expect = 9e-13
Identities = 59/217 (27%), Positives = 102/217 (47%), Gaps = 16/217 (7%)
Query: 63 EVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSE 122
+ G M + +Q K+ + D+++ +VD R L ++ + +++ P +LV+NK++
Sbjct: 15 QWFPGHMKKAKRQLKEVLKSVDVVVEVVDARDPLGTRNPELERIVKEK--PKLLVLNKAD 72
Query: 123 NINSSI---SLDFYELGIGNPHI-ISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIH 178
+ +++ G I +SA G K + + + K KKK
Sbjct: 73 LAPKEVTKKWKKYFKKEEGIKPIFVSAKSRQGGKKIRKALEKLSEEKIKRLKKK----GL 128
Query: 179 SIEYIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTA 238
I+V +VG PNVGKSTLIN LLG+ T + PGTT+ + ++ Y L+DT
Sbjct: 129 LKRKIRVGVVGYPNVGKSTLINRLLGKKVAKTSNRPGTTKG--IQWIKLDDGIY-LLDTP 185
Query: 239 GI--RRRNKTFEVIEKFSVIKTLK-SILEANVVILLL 272
GI + + V+ K + +K +L A+ V L
Sbjct: 186 GIIPPKFDDDELVLLKLAPKGEIKDPVLPADEVAERL 222
Score = 50.8 bits (122), Expect = 2e-06
Identities = 25/95 (26%), Positives = 41/95 (43%), Gaps = 13/95 (13%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGG------ 59
+VG PNVGKSTL NRL + A +N PG T+ + ++DT G
Sbjct: 136 GVVGYPNVGKSTLINRLLGKKVAKTSNRPGTTKGIQW---IKLDDGIYLLDTPGIIPPKF 192
Query: 60 -FEPEVKKGIMHEMTKQTKQAIIESD-IIIFIVDG 92
+ V + + K ++ +D + ++ G
Sbjct: 193 DDDELVLLKLA--PKGEIKDPVLPADEVAERLLGG 225
>gnl|CDD|183413 PRK12295, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 373
Score = 70.7 bits (174), Expect = 1e-12
Identities = 39/122 (31%), Positives = 56/122 (45%), Gaps = 14/122 (11%)
Query: 865 QLSGEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMF 924
LSGE DI ++ ++ DE NG+ L LRP+ T V R I P R Y G +F
Sbjct: 39 DLSGE--DI-RRRIFVTSDE-NGEELCLRPDFTIPVCRRHIATAG--GEPARYAYLGEVF 92
Query: 925 RHERPQYGRYRQFYQIGVEAIGFPGPDI---DAELIIMCSRLWKNLNLKNICLELNSIGN 981
R R R +F Q G+E+ G D DAE++ + L ++ + L +G
Sbjct: 93 RQRR---DRASEFLQAGIESFG--RADPAAADAEVLALALEALAALGPGDLEVRLGDVGL 147
Query: 982 FN 983
F
Sbjct: 148 FA 149
Score = 53.8 bits (130), Expect = 3e-07
Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 1072 RGMDYYNRTVFEWTTDKLGSQNSICGGGRYDFLIKKF-SNKFVPASGFAIGIERL 1125
R +DYY VFE G + GGGRYD L+ + + + +PA GF+I ++RL
Sbjct: 314 RPLDYYTGFVFEIRAAGNGDPP-LAGGGRYDGLLTRLGAGEPIPAVGFSIWLDRL 367
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. These proteins are found in bacteria,
eukaryotes, and archaea. They all exhibit a circular
permutation of the GTPase signature motifs so that the
order of the conserved G box motifs is G4-G5-G1-G2-G3,
with G4 and G5 being permuted from the C-terminal region
of proteins in the Ras superfamily to the N-terminus of
YlqF-related GTPases.
Length = 146
Score = 65.9 bits (161), Expect = 2e-12
Identities = 44/162 (27%), Positives = 71/162 (43%), Gaps = 21/162 (12%)
Query: 84 DIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKS-----ENINSSISLDFYELGIG 138
D+++ +VD R L ++ I + + + +++V+NK+ E + ++ G
Sbjct: 1 DVVVEVVDARDPLSSRNPDIEVLINEKNKKLIMVLNKADLVPKEVLRKWVAELSELYGTK 60
Query: 139 NPHIISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIHSIEYIKVAIVGKPNVGKSTL 198
I SA G GI I K K I+V +VG PNVGKS+
Sbjct: 61 TFFI-SATNGQGILKLKAEI--------TKQKLKLKYKKG----IRVGVVGLPNVGKSSF 107
Query: 199 INSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGI 240
IN+LL + ++ PGTT+ +K+ L DT GI
Sbjct: 108 INALLNKFKLKVGSIPGTTKLQQDVKL---DKEIYLYDTPGI 146
Score = 35.1 bits (81), Expect = 0.067
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLTRD 39
+VG PNVGKS+ N L N V + PG T+
Sbjct: 96 VVGLPNVGKSSFINALLNKFKLKVGSIPGTTKL 128
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 66.1 bits (162), Expect = 4e-12
Identities = 45/162 (27%), Positives = 63/162 (38%), Gaps = 43/162 (26%)
Query: 102 LITNFLRKSG-QPIVLVINKSENINSSISLDFYE-----------LGIGNPHIISALYGN 149
LI G +P++LV NK + + + + + L I + ++SA G
Sbjct: 50 LIPGLAELIGAKPVILVGNKIDLLPKDVKPNRLKQWVKKRLKIGGLKIKDVILVSAKKGW 109
Query: 150 GIKNFLENILTIELPYKKFFKKKEFTNIHSIEYIKVAIVGKPNVGKSTLINSLLGEN--- 206
G++ +E I Y+ V +VG NVGKSTLIN+LL N
Sbjct: 110 GVEELIEEIKK-LAKYRG----------------DVYVVGATNVGKSTLINALLKSNGGK 152
Query: 207 --------RVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGI 240
R+ PGTT IK K L DT GI
Sbjct: 153 VQAQALVQRLTVSPIPGTTLGLIKIPLGEGKK---LYDTPGI 191
Score = 38.4 bits (90), Expect = 0.009
Identities = 19/66 (28%), Positives = 24/66 (36%), Gaps = 16/66 (24%)
Query: 7 LVGRPNVGKSTLFNRLTNS-----------RDALVANYPGLTRD-RHYGEGYIGKKSFII 54
+VG NVGKSTL N L S + V+ PG T + +
Sbjct: 130 VVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGLIKIP----LGEGKKL 185
Query: 55 IDTGGF 60
DT G
Sbjct: 186 YDTPGI 191
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 67.5 bits (166), Expect = 4e-12
Identities = 49/179 (27%), Positives = 85/179 (47%), Gaps = 16/179 (8%)
Query: 67 GIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSENINS 126
G M + ++ K+ + D++I ++D R L ++ +I +P ++V+NK++ +
Sbjct: 6 GHMAKARREIKEKLKLVDVVIEVLDARIPLSSRNPMIDEIRG--NKPRLIVLNKADLADP 63
Query: 127 SIS---LDFYELGIGNPHIISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIHSIEYI 183
+++ L ++E I+A G G+K ++ + + K K N I
Sbjct: 64 AVTKQWLKYFEEKGIKALAINAKKGKGVKKIIKAAKKLLKEKNEKLKAKGLLNRP----I 119
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDS--IKSLFEYNNKKYILIDTAGI 240
+ IVG PNVGKSTLIN L G+ + PG T+ IK + L+DT GI
Sbjct: 120 RAMIVGIPNVGKSTLINRLAGKKVAKVGNRPGVTKGQQWIKL-----SDGLELLDTPGI 173
Score = 47.1 bits (113), Expect = 3e-05
Identities = 19/33 (57%), Positives = 24/33 (72%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYPGLTR 38
++VG PNVGKSTL NRL + A V N PG+T+
Sbjct: 122 MIVGIPNVGKSTLINRLAGKKVAKVGNRPGVTK 154
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 69.8 bits (171), Expect = 5e-12
Identities = 54/219 (24%), Positives = 97/219 (44%), Gaps = 27/219 (12%)
Query: 9 GRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGFEPEVKKGI 68
G PNVGKSTLFN LT + V N+PG+T ++ G+ + I+D G
Sbjct: 1 GNPNVGKSTLFNALTGAN-QTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPG--------- 50
Query: 69 MHEMTKQTKQAII--------ESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINK 120
++ +T + + + + D+++ +VD +E++ +T L + G P++L +N
Sbjct: 51 IYSLTTFSLEEEVARDYLLNEKPDLVVNVVDASN--LERNLYLTLQLLELGIPMILALNL 108
Query: 121 ---SENINSSISLDFYELGIGNPHI-ISALYGNGIKNFLENI-LTIELPYKKFFKKKEFT 175
+E I + E +G P + SA G GI+ + I I L K +
Sbjct: 109 VDEAEKKGIRIDEEKLEERLGVPVVPTSATEGRGIERLKDAIRKAIGLKELKKRAIEIVP 168
Query: 176 NIHSI-EYIKVAIVGKPNVGKSTL-INSLLGENRVITYD 212
+ + E ++ I ++ K L I L E+ + +
Sbjct: 169 EAYQVVEVVEGLIEIIYSISKRGLEILLGLLEDLSLEIE 207
Score = 54.4 bits (131), Expect = 3e-07
Identities = 36/137 (26%), Positives = 66/137 (48%), Gaps = 19/137 (13%)
Query: 189 GKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRRRNKTFE 248
G PNVGKSTL N+L G N+ + + PG T + + + + ++D GI TF
Sbjct: 1 GNPNVGKSTLFNALTGANQTVG-NWPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLT-TFS 58
Query: 249 VIEKFSVIKTLKSILEANVVILLLDAQQ---NI--SAQDINIANFIYESGRSLIVCVNKW 303
+ E+ V + + ++V+ ++DA N+ + Q + E G +I+ +N
Sbjct: 59 LEEE--VARDYLLNEKPDLVVNVVDASNLERNLYLTLQ-------LLELGIPMILALNLV 109
Query: 304 DSIIHNQRKIIKNNIKK 320
D ++K I+ + +K
Sbjct: 110 DE---AEKKGIRIDEEK 123
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 66.7 bits (164), Expect = 1e-11
Identities = 54/181 (29%), Positives = 90/181 (49%), Gaps = 20/181 (11%)
Query: 67 GIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSENINS 126
G M + ++ K+ + D++I ++D R L ++ +I + +P +L++NKS+ +
Sbjct: 9 GHMAKARREIKENLKLVDVVIEVLDARIPLSSENPMIDKII--GNKPRLLILNKSDLADP 66
Query: 127 SIS---LDFYE-LGIGNPHIISALYGNGIKNFLENILTIELPYK-KFFKKKEFTNIHSIE 181
++ ++++E GI I+A G G+K L+ + L K + K K
Sbjct: 67 EVTKKWIEYFEEQGI-KALAINAKKGQGVKKILKAAKKL-LKEKNERRKAKGMRPRA--- 121
Query: 182 YIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDS--IKSLFEYNNKKYILIDTAG 239
I+ I+G PNVGKSTLIN L G+ T + PG T+ IK K L+DT G
Sbjct: 122 -IRAMIIGIPNVGKSTLINRLAGKKIAKTGNRPGVTKAQQWIKL-----GKGLELLDTPG 175
Query: 240 I 240
I
Sbjct: 176 I 176
Score = 46.7 bits (112), Expect = 4e-05
Identities = 17/33 (51%), Positives = 23/33 (69%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYPGLTR 38
+++G PNVGKSTL NRL + A N PG+T+
Sbjct: 125 MIIGIPNVGKSTLINRLAGKKIAKTGNRPGVTK 157
>gnl|CDD|239880 cd04418, NDPk5, Nucleoside diphosphate kinase homolog 5 (NDP kinase
homolog 5, NDPk5, NM23-H5; Inhibitor of p53-induced
apoptosis-beta, IPIA-beta): In human, mRNA for NDPk5 is
almost exclusively found in testis, especially in the
flagella of spermatids and spermatozoa, in association
with axoneme microtubules, and may play a role in
spermatogenesis by increasing the ability of late-stage
spermatids to eliminate reactive oxygen species. It
belongs to the nm23 Group II genes and appears to differ
from the other human NDPks in that it lacks two
important catalytic site residues, and thus does not
appear to possess NDP kinase activity. NDPk5 confers
protection from cell death by Bax and alters the
cellular levels of several antioxidant enzymes,
including glutathione peroxidase 5 (Gpx5).
Length = 132
Score = 62.8 bits (153), Expect = 1e-11
Identities = 37/116 (31%), Positives = 58/116 (50%), Gaps = 7/116 (6%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKNRPFFKNLV 481
RT ++I DA+ K EI + + G I+ +LS FY+ H + FF +LV
Sbjct: 2 RTLAIIKPDAVHKA--EEIEDIILESGFTIVQKRKLQLSPEQCSDFYAEHYGKMFFPHLV 59
Query: 482 NFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKA---AKGTIRADFAESIDKNIVH 534
+M SGP+ VL +AI + L+G T+ +KA ++RA + +N VH
Sbjct: 60 AYMSSGPIVAMVLARHNAISYWKELLGPTNSLKAKETHPDSLRAIYGTDDLRNAVH 115
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 63.4 bits (155), Expect = 4e-11
Identities = 44/175 (25%), Positives = 77/175 (44%), Gaps = 26/175 (14%)
Query: 181 EYIKVAIVGKPNVGKSTLINSLLGENRVI-TYDTPGTTRDSIKSLFEYNNKKYILIDTAG 239
+ ++A G+ NVGKS+LIN+L + + T TPG T+ FE +++ L+D G
Sbjct: 23 DLPEIAFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQLIN--FFEVDDELR-LVDLPG 79
Query: 240 -----------IRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANF 288
+ + E +EK + +K V+LL+DA+ D + F
Sbjct: 80 YGYAKVPKEVKEKWKKLIEEYLEKRANLK---------GVVLLIDARHPPKDLDREMIEF 130
Query: 289 IYESGRSLIVCVNKWDSIIHNQRKIIKNNIKKKLNF--LSFAMFNFISAIKLNNI 341
+ E G +IV + K D + ++R N + ++L S++K I
Sbjct: 131 LLELGIPVIVVLTKADKLKKSERNKQLNKVAEELKKPPPDDQWVVLFSSLKKKGI 185
Score = 63.0 bits (154), Expect = 6e-11
Identities = 39/177 (22%), Positives = 74/177 (41%), Gaps = 24/177 (13%)
Query: 2 KPVLVLVGRPNVGKSTLFNRLTNSRD-ALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGF 60
P + GR NVGKS+L N LTN ++ A + PG T+ ++ + ++D G+
Sbjct: 24 LPEIAFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQLINF---FEVDDELRLVDLPGY 80
Query: 61 -----EPEVKKGIMHEMTK--QTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQP 113
EVK+ + + + + + ++ ++D R + D+ + FL + G P
Sbjct: 81 GYAKVPKEVKEKWKKLIEEYLEKRANL---KGVVLLIDARHPPKDLDREMIEFLLELGIP 137
Query: 114 IVLVINKSENINSSI----------SLDFYELGIGNPHIISALYGNGIKNFLENILT 160
+++V+ K++ + S L + S+L GI IL
Sbjct: 138 VIVVLTKADKLKKSERNKQLNKVAEELKKPPPDDQWVVLFSSLKKKGIDELKAKILE 194
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 65.3 bits (160), Expect = 6e-11
Identities = 73/266 (27%), Positives = 104/266 (39%), Gaps = 55/266 (20%)
Query: 109 KSGQPIVLVINK---------SENINSSISLDFYELGIGNPHII--SALYGNGIKNFLEN 157
G P++LV NK I + ELG+ II SA GNGI L+
Sbjct: 88 VGGNPVLLVGNKIDLLPKSVNLSKIKEWMKKRAKELGLKPVDIILVSAKKGNGIDELLDK 147
Query: 158 ILTIELPYKKFFKKKEFTNIHSIEYIKVAIVGKPNVGKSTLINSLLGEN----RVITYDT 213
I KK KK V +VG NVGKS+LIN LL +N VIT
Sbjct: 148 I-------KKARNKK-----------DVYVVGVTNVGKSSLINKLLKQNNGDKDVITTSP 189
Query: 214 -PGTTRDSIKSLFEYNNKKYILIDTAGIRRRNKTFEVIEKFSVIKTLKSIL---EANVVI 269
PGTT D I+ + + L DT GI ++ ++K K LK I E
Sbjct: 190 FPGTTLDLIEIPLDDGH---SLYDTPGIINSHQMAHYLDK----KDLKYITPKKEIKPKT 242
Query: 270 LLLDAQQNISAQDINIANFIYESG--RSLIVCVNKWDSIIHNQRKIIKNNIKKKLNFLSF 327
L+ Q + +A F Y G S V+ N+ I + ++ +
Sbjct: 243 YQLNPNQTLFLG--GLARFDYLKGEKTSFTFYVS-------NELNIHRTKLENADELYNK 293
Query: 328 AMFNFISAIKLNNINSFMESINHVYD 353
+ N +S L++ + E + H +
Sbjct: 294 HLGNLLSPPCLDDKFNLPELVFHTFT 319
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes [Protein synthesis, Other].
Length = 178
Score = 62.1 bits (152), Expect = 7e-11
Identities = 43/162 (26%), Positives = 76/162 (46%), Gaps = 18/162 (11%)
Query: 185 VAIVGKPNVGKSTLINSLLGENR-VITYDTPGTTRDSIKSLFEYNNKKYILIDTAG---- 239
+A G+ NVGKS+LIN+L + T TPG T+ I + FE N+ L+D G
Sbjct: 21 IAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQ-LI-NFFEVNDGFR-LVDLPGYGYA 77
Query: 240 ---IRRRNKTFEVIEKFSVI-KTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRS 295
+ K ++IE++ + LK V+LL+D + + D+ + ++ E G
Sbjct: 78 KVSKEEKEKWQKLIEEYLEKRENLKG------VVLLMDIRHPLKELDLEMIEWLRERGIP 131
Query: 296 LIVCVNKWDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIK 337
+++ + K D + ++ IKK L + S++K
Sbjct: 132 VLIVLTKADKLKKSELNKQLKKIKKALKKDADDSVQLFSSLK 173
Score = 50.2 bits (121), Expect = 8e-07
Identities = 33/129 (25%), Positives = 64/129 (49%), Gaps = 14/129 (10%)
Query: 7 LVGRPNVGKSTLFNRLTNSRD-ALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGF----- 60
GR NVGKS+L N LTN + A + PG T+ ++ + F ++D G+
Sbjct: 23 FAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINF---FEVNDGFRLVDLPGYGYAKV 79
Query: 61 EPEVKKGIMHEMTK--QTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVI 118
E K+ + + + ++ + ++ ++D R L E D + +LR+ G P+++V+
Sbjct: 80 SKEEKEKWQKLIEEYLEKRENLKG---VVLLMDIRHPLKELDLEMIEWLRERGIPVLIVL 136
Query: 119 NKSENINSS 127
K++ + S
Sbjct: 137 TKADKLKKS 145
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 61.3 bits (150), Expect = 2e-10
Identities = 46/169 (27%), Positives = 78/169 (46%), Gaps = 33/169 (19%)
Query: 185 VAIVGKPNVGKSTLINSLLGENR-VITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRRR 243
+A G+ NVGKS+LIN+L T TPG T+ I + FE N+K L+D G
Sbjct: 27 IAFAGRSNVGKSSLINALTNRKNLARTSKTPGRTQ-LI-NFFEVNDKLR-LVDLPG---- 79
Query: 244 NKTF-------EVIEKFSVI--------KTLKSILEANVVILLLDAQQNISAQDINIANF 288
+ E EK+ + + LK V+LL+D++ + D+ + +
Sbjct: 80 ---YGYAKVSKEEKEKWQKLIEEYLRTRENLK------GVVLLIDSRHPLKELDLQMIEW 130
Query: 289 IYESGRSLIVCVNKWDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIK 337
+ E G +++ + K D + +RK ++K L F + F S++K
Sbjct: 131 LKEYGIPVLIVLTKADKLKKGERKKQLKKVRKALKFGDDEVILF-SSLK 178
Score = 51.3 bits (124), Expect = 4e-07
Identities = 39/171 (22%), Positives = 76/171 (44%), Gaps = 21/171 (12%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRD-ALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGF---- 60
GR NVGKS+L N LTN ++ A + PG T+ ++ + ++D G+
Sbjct: 28 AFAGRSNVGKSSLINALTNRKNLARTSKTPGRTQLINF---FEVNDKLRLVDLPGYGYAK 84
Query: 61 -EPEVKKGIMHEMTK--QTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLV 117
E K+ + + +T++ + ++ ++D R L E D + +L++ G P+++V
Sbjct: 85 VSKEEKEKWQKLIEEYLRTRENLK---GVVLLIDSRHPLKELDLQMIEWLKEYGIPVLIV 141
Query: 118 INKSENINSS-----ISLDFYELGIGNPHII--SALYGNGIKNFLENILTI 161
+ K++ + + L G+ +I S+L GI I
Sbjct: 142 LTKADKLKKGERKKQLKKVRKALKFGDDEVILFSSLKKQGIDELRAAIAKW 192
>gnl|CDD|238391 cd00768, class_II_aaRS-like_core, Class II tRNA amino-acyl
synthetase-like catalytic core domain. Class II amino
acyl-tRNA synthetases (aaRS) share a common fold and
generally attach an amino acid to the 3' OH of ribose of
the appropriate tRNA. PheRS is an exception in that it
attaches the amino acid at the 2'-OH group, like class I
aaRSs. These enzymes are usually homodimers. This domain
is primarily responsible for ATP-dependent formation of
the enzyme bound aminoacyl-adenylate. The substrate
specificity of this reaction is further determined by
additional domains. Intererestingly, this domain is also
found is asparagine synthase A (AsnA), in the accessory
subunit of mitochondrial polymerase gamma and in the
bacterial ATP phosphoribosyltransferase regulatory
subunit HisZ.
Length = 211
Score = 60.2 bits (146), Expect = 5e-10
Identities = 35/121 (28%), Positives = 51/121 (42%), Gaps = 8/121 (6%)
Query: 867 SGEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMFRH 926
E+ K++ E D L LRP ++R + I P RL GP FR+
Sbjct: 31 LLEKAGHEPKDLLPVGAENEED-LYLRPTLEPGLVRLF--VSHIRKLPLRLAEIGPAFRN 87
Query: 927 ERPQYG--RYRQFYQIGVEAIGFPGPD--IDAELIIMCSRLWKNLNLK-NICLELNSIGN 981
E + G R R+F Q+ E G G + ELI + L + L +K +I + G
Sbjct: 88 EGGRRGLRRVREFTQLEGEVFGEDGEEASEFEELIELTEELLRALGIKLDIVFVEKTPGE 147
Query: 982 F 982
F
Sbjct: 148 F 148
Score = 32.1 bits (73), Expect = 1.5
Identities = 16/62 (25%), Positives = 21/62 (33%), Gaps = 11/62 (17%)
Query: 1075 DYYNRTVFEWTTD-KLGSQNSICGGGRY----------DFLIKKFSNKFVPASGFAIGIE 1123
FE D G I GG FL + ++ P GF +G+E
Sbjct: 150 PGGAGPGFEIEVDHPEGRGLEIGSGGYRQDEQARAADLYFLDEALEYRYPPTIGFGLGLE 209
Query: 1124 RL 1125
RL
Sbjct: 210 RL 211
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 59.8 bits (146), Expect = 6e-10
Identities = 47/172 (27%), Positives = 79/172 (45%), Gaps = 23/172 (13%)
Query: 3 PVLVLVGRPNVGKSTLFNRLTNSRDALVANY------PGLTRDRHYGEGYIGKKSFIIID 56
P + LVG N GKSTLFN LT + D L + P TR G + ++ D
Sbjct: 42 PTVALVGYTNAGKSTLFNALTGA-DVLAEDQLFATLDP-TTRRIKLP----GGREVLLTD 95
Query: 57 TGGFEPEVKKGIMHEMT---KQTKQAIIESDIIIFIVDG----RQGLVEQDKLITNFLRK 109
T GF ++ + H++ + T + + E+D+++ +VD R+ +E + + L
Sbjct: 96 TVGF---IRD-LPHQLVEAFRSTLEEVAEADLLLHVVDASDPDREEQIETVEEVLKELGA 151
Query: 110 SGQPIVLVINKSENINSSISLDFYELGIGNPHIISALYGNGIKNFLENILTI 161
PI+LV+NK + ++ + G + ISA G G+ E I +
Sbjct: 152 DDIPIILVLNKIDLLDDEELEERLRAGRPDAVFISAKTGEGLDLLKEAIEEL 203
Score = 47.5 bits (114), Expect = 9e-06
Identities = 36/142 (25%), Positives = 63/142 (44%), Gaps = 43/142 (30%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVI------TYDTPGTTRDSIKSLFEYNNKKYILIDTA 238
VA+VG N GKSTL N+L G + + T D TTR + ++ +L DT
Sbjct: 44 VALVGYTNAGKSTLFNALTGADVLAEDQLFATLDP--TTR----RIKLPGGREVLLTDTV 97
Query: 239 GIRRRNKTF------EVIEKFSVIKTLKSILEANVVILLLDA-----QQNISA-----QD 282
G F +++E F TL+ + EA++++ ++DA ++ I ++
Sbjct: 98 G-------FIRDLPHQLVEAFRS--TLEEVAEADLLLHVVDASDPDREEQIETVEEVLKE 148
Query: 283 INIANFIYESGRSLIVCVNKWD 304
+ + ++V NK D
Sbjct: 149 LGA-----DDIPIILVL-NKID 164
>gnl|CDD|217866 pfam04055, Radical_SAM, Radical SAM superfamily. Radical SAM
proteins catalyze diverse reactions, including unusual
methylations, isomerisation, sulphur insertion, ring
formation, anaerobic oxidation and protein radical
formation.
Length = 165
Score = 58.7 bits (142), Expect = 9e-10
Identities = 32/184 (17%), Positives = 69/184 (37%), Gaps = 29/184 (15%)
Query: 620 ISTQVGCAINCIFCSTGRQGF---VRNLTVGEIIGQLWVTEFKLRREKNIKINSQGKRQI 676
I GC + C +C+ R L+ EI+ + + R
Sbjct: 1 IIVTRGCNLRCTYCAFPSIRARGKGRELSPEEILEEAK----------------ELARLG 44
Query: 677 TNIVMMGMGEPLLNYKSTIGALKLILSDHAYGLSRRHVILSTSGIIP---MIDKLAQECP 733
+V++ GEPLL +L+ G + L T+G + ++++L +
Sbjct: 45 VEVVILTGGEPLLLPDLVELLERLLKLREGEG---IRITLETNGTLLDEELLEELKEAGL 101
Query: 734 VELAVSLHASNNNLRNKLVPISKKYPLKELILACHRYITYSPRHMITFEYCMLHGINDTD 793
+++SL + ++ + I++ + +E +L + + ++ L G ND D
Sbjct: 102 DRVSISLQSGDDEVLK---IINRGHTFEE-VLEALELLREAGIPVVVDNIVGLPGENDED 157
Query: 794 IHAI 797
+
Sbjct: 158 LEET 161
>gnl|CDD|239875 cd04412, NDPk7B, Nucleoside diphosphate kinase 7 domain B (NDPk7B):
The nm23-H7 class of nucleoside diphosphate kinase
(NDPk7) consists of an N-terminal DM10 domain and two
functional catalytic NDPk modules, NDPk7A and NDPk7B.
The function of the DM10 domain, which also occurs in
multiple copies in other proteins, is unknown. NDPk7 is
predominantly expressed in testes, although appreciable
amount are also found in liver, heart, brain, ovary,
small intestine and spleen. The nm23-H7 gene is located
in or near the hereditary prostrate cancer
susceptibility locus. Nm23-H7 may be involved in the
development of colon and gastric carcinoma, the latter
possibly in a type-specific manner.
Length = 134
Score = 57.3 bits (139), Expect = 1e-09
Identities = 35/118 (29%), Positives = 58/118 (49%), Gaps = 8/118 (6%)
Query: 424 RTFSLI--DALEKNIVGEIYNRYEKIGLKIIAAYMKKLSKNDVEKFYSIHKN-RPFFKNL 480
T +I A+ ++GEI + G +I A M L++ + E+F ++K P +
Sbjct: 2 CTVCIIKPHAVSHGLLGEILQQILDEGFEITALQMFNLTRANAEEFLEVYKGVVPELPAM 61
Query: 481 VNFMISGPVFIQVLEGEDAIKKHRILIGDTDPIKAAK----GTIRADFAESIDKNIVH 534
V+ + SGP + GE+A+K R G DP + AK T+RA + + +N VH
Sbjct: 62 VDELTSGPCIALEIAGENAVKTFREFCGPFDP-EIAKQLRPNTLRARYGKDKVQNAVH 118
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. Human HSR1 is localized to the human MHC class
I region and is highly homologous to a putative
GTP-binding protein, MMR1 from mouse. These proteins
represent a new subfamily of GTP-binding proteins that
has only eukaryote members. This subfamily shows a
circular permutation of the GTPase signature motifs so
that the C-terminal strands 5, 6, and 7 (strand 6
contains the G4 box with sequence NKXD) are relocated to
the N-terminus.
Length = 140
Score = 56.5 bits (137), Expect = 2e-09
Identities = 34/138 (24%), Positives = 56/138 (40%), Gaps = 33/138 (23%)
Query: 83 SDIIIFIVDGRQGLVEQDKLITNFLRKSGQ--PIVLVINKSENINSSISLDFYELGIGNP 140
SD+++ IVD R L + + ++++ VL++NK++ + +
Sbjct: 12 SDVVVQIVDARNPLFFRCPDLEKYVKEVDPSKENVLLLNKADLVTEEQRKAWAR------ 65
Query: 141 HIISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIHSIEYIKVAIVGKPNVGKSTLIN 200
GI F E T + +VG PNVGKS+LIN
Sbjct: 66 ----YFKKEGIVVLF------------FSALNEAT---------IGLVGYPNVGKSSLIN 100
Query: 201 SLLGENRVITYDTPGTTR 218
+L+G +V TPG T+
Sbjct: 101 ALVGSKKVSVSSTPGKTK 118
Score = 35.7 bits (83), Expect = 0.044
Identities = 17/38 (44%), Positives = 24/38 (63%)
Query: 1 MKPVLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTR 38
+ + LVG PNVGKS+L N L S+ V++ PG T+
Sbjct: 81 NEATIGLVGYPNVGKSSLINALVGSKKVSVSSTPGKTK 118
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 58.6 bits (143), Expect = 8e-09
Identities = 48/172 (27%), Positives = 71/172 (41%), Gaps = 30/172 (17%)
Query: 3 PVLVLVGRPNVGKSTLFNRLTNSR----DALVANYPGLTRDRHYGEGYIGKKSFIIIDTG 58
P + LVG N GKSTLFN LT + D L A TR +G ++ DT
Sbjct: 190 PTVALVGYTNAGKSTLFNALTGADVYAADQLFATLDPTTRRLDLPDGG----EVLLTDTV 245
Query: 59 GFEPEVKKGIMH------EMTKQTKQAIIESDIIIFIVD----GRQGLVEQDKLITNFLR 108
GF I + T + + E+D+++ +VD R+ +E + + L
Sbjct: 246 GF-------IRDLPHELVAAFRATLEEVREADLLLHVVDASDPDREEQIEAVEKVLEELG 298
Query: 109 KSGQPIVLVINKSENINSSISLDFYELGIGNPHI--ISALYGNGIKNFLENI 158
P +LV NK + ++ L G P +SA G G+ LE I
Sbjct: 299 AEDIPQLLVYNKIDLLDEP---RIERLEEGYPEAVFVSAKTGEGLDLLLEAI 347
Score = 40.9 bits (97), Expect = 0.003
Identities = 41/138 (29%), Positives = 66/138 (47%), Gaps = 33/138 (23%)
Query: 184 KVAIVGKPNVGKSTLINSLLG-----ENRVI-TYDTPGTTRDSIKSLFEYNNKKYILIDT 237
VA+VG N GKSTL N+L G +++ T D TTR L + + +L DT
Sbjct: 191 TVALVGYTNAGKSTLFNALTGADVYAADQLFATLDP--TTRR----LDLPDGGEVLLTDT 244
Query: 238 AG-IRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDA-----QQNISA-----QDINIA 286
G I R+ E++ F TL+ + EA++++ ++DA ++ I A +++
Sbjct: 245 VGFI--RDLPHELVAAFR--ATLEEVREADLLLHVVDASDPDREEQIEAVEKVLEELGA- 299
Query: 287 NFIYESGRSLIVCVNKWD 304
E L+V NK D
Sbjct: 300 ----EDIPQLLVY-NKID 312
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 56.1 bits (136), Expect = 1e-08
Identities = 47/188 (25%), Positives = 77/188 (40%), Gaps = 33/188 (17%)
Query: 185 VAIVGKPNVGKSTLINSLLGEN-----RVITYDTPGTTRD-------SIKS---LFEYNN 229
V ++G + GK+TL SLL + R +T T +IK+ FE+
Sbjct: 2 VGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWPK 61
Query: 230 KKYILIDTAGIRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFI 289
++ IDT G E FS +T++ + +A+ +L++DA + + Q N
Sbjct: 62 RRINFIDTPGH----------EDFS-KETVRGLAQADGALLVVDANEGVEPQTREHLNIA 110
Query: 290 YESGRSLIVCVNKWDSIIHNQRKIIKNNIKKKLN-----FLSFAMFN--FISAIKLNNIN 342
G +IV VNK D + + IK+ L FL ISA+ I
Sbjct: 111 LAGGLPIIVAVNKIDRVGEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTGEGIE 170
Query: 343 SFMESINH 350
+++I
Sbjct: 171 ELLDAIVE 178
Score = 47.7 bits (114), Expect = 6e-06
Identities = 41/189 (21%), Positives = 67/189 (35%), Gaps = 39/189 (20%)
Query: 7 LVGRPNVGKSTLFNRLT-----NSRDALVANYP----------GLTRDRHYGEGYIGKKS 51
++G + GK+TL L R G+T E K+
Sbjct: 4 VIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWPKRR 63
Query: 52 FIIIDTGGFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSG 111
IDT G E +K+T + + ++D + +VD +G+ Q + N G
Sbjct: 64 INFIDTPGHED---------FSKETVRGLAQADGALLVVDANEGVEPQTREHLNIALAGG 114
Query: 112 QPIVLVINKS---------------ENINSSISLDFYELGIGNPHIISALYGNGIKNFLE 156
PI++ +NK + + I F + ISAL G GI+ L+
Sbjct: 115 LPIIVAVNKIDRVGEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTGEGIEELLD 174
Query: 157 NILTIELPY 165
I+ P
Sbjct: 175 AIVEHLPPP 183
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 55.5 bits (134), Expect = 1e-08
Identities = 51/171 (29%), Positives = 72/171 (42%), Gaps = 26/171 (15%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGK-KSFIIIDTGGFEPEV 64
LVG PNVGKSTL + LT S +A+YP T + + G G IID G
Sbjct: 1 GLVGLPNVGKSTLLSALT-SAKVEIASYPFTTLEPNVGVFEFGDGVDIQIIDLPGLLDGA 59
Query: 65 KKGIMHEMTKQTKQAII----ESDIIIFIVD-----GRQGLVEQDKLITN----FLRKSG 111
+G + + I+ SD+I+ ++D L +Q L FL
Sbjct: 60 SEG------RGLGEQILAHLYRSDLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKN 113
Query: 112 QPIVLVINK----SENINSSISLDFYELGIGNPHIISALYGNGIKNFLENI 158
+P ++V NK SEN + LD + GI SAL G+ + I
Sbjct: 114 KPEMIVANKIDMASENNLKRLKLDKLKRGI-PVVPTSALTRLGLDRVIRTI 163
Score = 46.2 bits (110), Expect = 1e-05
Identities = 33/155 (21%), Positives = 70/155 (45%), Gaps = 20/155 (12%)
Query: 186 AIVGKPNVGKSTLINSLLGEN-RVITYDTPGTTRDSIKSLFEYNN-KKYILIDTAG-IRR 242
+VG PNVGKSTL+++L + +Y P TT + +FE+ + +ID G +
Sbjct: 1 GLVGLPNVGKSTLLSALTSAKVEIASY--PFTTLEPNVGVFEFGDGVDIQIIDLPGLLDG 58
Query: 243 RNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISA---QDINIAN------FIYESG 293
++ + E+ L + +++++ ++DA ++ +D N F++
Sbjct: 59 ASEGRGLGEQI-----LAHLYRSDLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKN 113
Query: 294 RSLIVCVNKWDSIIHNQRKI-IKNNIKKKLNFLSF 327
+ ++ NK D N K + +K+ + +
Sbjct: 114 KPEMIVANKIDMASENNLKRLKLDKLKRGIPVVPT 148
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 54.9 bits (133), Expect = 2e-08
Identities = 42/158 (26%), Positives = 72/158 (45%), Gaps = 16/158 (10%)
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYI-LIDTAGIRR 242
+A+VG+ + GKSTL+N+LLGE + T TP TT ++ ++ Y K + L+DT G+
Sbjct: 2 LLAVVGEFSAGKSTLLNALLGEEVLPTGVTP-TT--AVITVLRYGLLKGVVLVDTPGLNS 58
Query: 243 RNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCV-N 301
+ I T + A+ VI +L A Q ++ + I + I V N
Sbjct: 59 TIEHHTEI-------TESFLPRADAVIFVLSADQPLTESEREFLKEILKWSGKKIFFVLN 111
Query: 302 KWDSIIHNQRKIIKNNIKKKLNFLSFAMFN----FISA 335
K D + + + + +++L L +SA
Sbjct: 112 KIDLLSEEELEEVLEYSREELGVLELGGGEPRIFPVSA 149
Score = 40.6 bits (96), Expect = 0.002
Identities = 42/166 (25%), Positives = 65/166 (39%), Gaps = 44/166 (26%)
Query: 5 LVLVGRPNVGKSTLFNRL------------TNSRDALVANYPGLTRDRHYGEGYIGKKSF 52
L +VG + GKSTL N L T + ++ YG K
Sbjct: 3 LAVVGEFSAGKSTLLNALLGEEVLPTGVTPTTAVITVLR----------YG----LLKGV 48
Query: 53 IIIDTGGFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDK-LITNFLRKSG 111
+++DT G + T+ T+ + +D +IF++ Q L E ++ + L+ SG
Sbjct: 49 VLVDTPGLN-----STIEHHTEITESFLPRADAVIFVLSADQPLTESEREFLKEILKWSG 103
Query: 112 QPIVLVINK----------SENINSSISLDFYELGIGNPHI--ISA 145
+ I V+NK S L ELG G P I +SA
Sbjct: 104 KKIFFVLNKIDLLSEEELEEVLEYSREELGVLELGGGEPRIFPVSA 149
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 54.2 bits (131), Expect = 2e-08
Identities = 44/178 (24%), Positives = 81/178 (45%), Gaps = 33/178 (18%)
Query: 74 KQTKQAII-ESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSENINSSISLDF 132
K+ + II E+D+++ +VD R + + + + + G+ +++V+NK++ + +
Sbjct: 2 KRLVRRIIKEADVVLEVVDARDPELTRSRKLERMALELGKKLIIVLNKAD----LVPREV 57
Query: 133 YE------LGIGNPHI-ISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIHSIEYIKV 185
E G P + +SA G + I + + K + V
Sbjct: 58 LEKWKEVFESEGLPVVYVSARERLGTRILRRTIKELAIDGKP---------------VIV 102
Query: 186 AIVGKPNVGKSTLINSLLGENRVIT---YDTPGTTRDSIKSLFEYNNKKYILIDTAGI 240
+VG P VGKS++IN+L G + T +PG T+ L ++K Y LIDT G+
Sbjct: 103 GVVGYPKVGKSSIINALKGRHSASTSPIPGSPGYTKG--IQLVRIDSKIY-LIDTPGV 157
Score = 35.0 bits (81), Expect = 0.087
Identities = 24/63 (38%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 2 KPVLV-LVGRPNVGKSTLFNRLTNSRDAL---VANYPGLTRDRHYGEGYIGKKSFI-IID 56
KPV+V +VG P VGKS++ N L A + PG T+ G + S I +ID
Sbjct: 98 KPVIVGVVGYPKVGKSSIINALKGRHSASTSPIPGSPGYTK----GIQLVRIDSKIYLID 153
Query: 57 TGG 59
T G
Sbjct: 154 TPG 156
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 54.5 bits (132), Expect = 3e-08
Identities = 48/175 (27%), Positives = 68/175 (38%), Gaps = 27/175 (15%)
Query: 3 PVLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGFEP 62
LV+ G PNVGKS+L N+LT + VA YP T+ G + +IDT P
Sbjct: 1 RTLVIAGYPNVGKSSLVNKLTRA-KPEVAPYPFTTKSLFVGHFDYKYLRWQVIDT----P 55
Query: 63 EVKKGI----MHEMTKQTKQAIIE----SDIIIFIVD--GRQG--LVEQDKLITNFLRKS 110
GI + E QAI ++F +D G + EQ L
Sbjct: 56 ----GILDRPLEERNTIEMQAITALAHLRAAVLFFIDPSETCGYSIEEQLSLFKEIKPLF 111
Query: 111 GQPIVLVINK---SENINSSISLDFYELGIGNPHIISALYGNGI---KNFLENIL 159
+P+++V+NK + S E IS L G+ KN +L
Sbjct: 112 NKPVIVVLNKIDLLTEEDLSEIEKELEKEGEEVIKISTLTEEGVDELKNKACELL 166
Score = 42.5 bits (101), Expect = 3e-04
Identities = 32/97 (32%), Positives = 44/97 (45%), Gaps = 17/97 (17%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLF----EYNNKKYILIDTAGI 240
+ I G PNVGKS+L+N L + P TT KSLF +Y ++ +IDT GI
Sbjct: 3 LVIAGYPNVGKSSLVNKLTR-AKPEVAPYPFTT----KSLFVGHFDYKYLRWQVIDTPGI 57
Query: 241 RRRNKTFE---VIEKFSVIKTLKSILEANVVILLLDA 274
R E IE + I L + V+ +D
Sbjct: 58 LDR--PLEERNTIEMQA-ITALAHL--RAAVLFFIDP 89
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 55.9 bits (134), Expect = 6e-08
Identities = 52/183 (28%), Positives = 88/183 (48%), Gaps = 21/183 (11%)
Query: 173 EFTNIHSIEYIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKY 232
+F + + + + V I+G+PN GKSTL+N ++GE I TTR I + + +
Sbjct: 43 KFGKMSNQKTVSVCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQV 102
Query: 233 ILIDTAGIRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYES 292
IL DT GI + +EK V S+ A++V+L++D+ ++ +I + I +
Sbjct: 103 ILYDTPGIFEPKGS---LEKAMVRCAWSSLHSADLVLLIIDSLKSFD----DITHNILDK 155
Query: 293 GRSL----IVCVNKWD---SIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFM 345
RSL I +NK D +++ + + N L F ISA+ NI+ +
Sbjct: 156 LRSLNIVPIFLLNKIDIESKYLNDIKAFLTENHPDSLLFP-------ISALSGKNIDGLL 208
Query: 346 ESI 348
E I
Sbjct: 209 EYI 211
Score = 43.5 bits (102), Expect = 4e-04
Identities = 45/160 (28%), Positives = 70/160 (43%), Gaps = 9/160 (5%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGG-FEPEVK 65
++GRPN GKSTL NR+ + ++V TR G + I+ DT G FEP K
Sbjct: 57 IIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPGIFEP--K 114
Query: 66 KGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSENIN 125
+ M + ++ +D+++ I+D + + I + LR + ++NK + I
Sbjct: 115 GSLEKAMVRCAWSSLHSADLVLLIIDSLKSFDDITHNILDKLRSLNIVPIFLLNKID-IE 173
Query: 126 SSISLDFYELGIGNP-----HIISALYGNGIKNFLENILT 160
S D N ISAL G I LE I +
Sbjct: 174 SKYLNDIKAFLTENHPDSLLFPISALSGKNIDGLLEYITS 213
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 55.4 bits (134), Expect = 8e-08
Identities = 52/163 (31%), Positives = 73/163 (44%), Gaps = 21/163 (12%)
Query: 3 PVLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGF-- 60
P +V+ G PNVGKS+L +LT + VA YP T+ H G G +IDT G
Sbjct: 169 PTIVVAGYPNVGKSSLVRKLTTA-KPEVAPYPFTTKGIHVGHFERGYLRIQVIDTPGLLD 227
Query: 61 EPEVKKGIMHEMTKQTKQAIIE----SDIIIFIVDGRQ----GLVEQDKLITNFLRKSGQ 112
P + E + +QAI+ + +I+F+ D + L EQ L+
Sbjct: 228 RP------LEERNEIERQAILALRHLAGVILFLFDPSETCGYSLEEQISLLEEIKELFKA 281
Query: 113 PIVLVINKSENINSS----ISLDFYELGIGNPHIISALYGNGI 151
PIV+VINK + + I E G P ISA G G+
Sbjct: 282 PIVVVINKIDIADEEKLEEIEASVLEEGGEEPLKISATKGCGL 324
Score = 40.4 bits (95), Expect = 0.005
Identities = 28/95 (29%), Positives = 44/95 (46%), Gaps = 13/95 (13%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGI---- 240
+ + G PNVGKS+L+ L + P TT+ FE + +IDT G+
Sbjct: 171 IVVAGYPNVGKSSLVRKLTTA-KPEVAPYPFTTKGIHVGHFERGYLRIQVIDTPGLLDRP 229
Query: 241 -RRRNKTFEVIEKFSVIKTLKSILEANVVILLLDA 274
RN+ IE+ + I L+ + A V++ L D
Sbjct: 230 LEERNE----IERQA-ILALRHL--AGVILFLFDP 257
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 54.7 bits (133), Expect = 1e-07
Identities = 49/182 (26%), Positives = 71/182 (39%), Gaps = 49/182 (26%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYP--------GLTRDRHYGEGYIGKKSFIIID-- 56
LVG PN GKSTL + ++ ++ +A+YP G+ R Y KSF+I D
Sbjct: 163 LVGLPNAGKSTLISAVSAAK-PKIADYPFTTLHPNLGVVRVDDY-------KSFVIADIP 214
Query: 57 -------TGGFEPEVKKGIMHEMTKQTKQAIIE-SDIIIFIVDG-RQGLVEQDKLITNFL 107
G G+ H K IE + +++ +VD VE K I N L
Sbjct: 215 GLIEGASEG-------AGLGHRFLKH-----IERTRLLLHLVDIEAVDPVEDYKTIRNEL 262
Query: 108 RKSGQ-----PIVLVINKS-----ENINSSISLDFYELGIGNPHIISALYGNGIKNFLEN 157
K P +LV+NK E + G +ISA+ G G+ L
Sbjct: 263 EKYSPELADKPRILVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVTGEGLDELLRA 322
Query: 158 IL 159
+
Sbjct: 323 LW 324
Score = 34.7 bits (81), Expect = 0.28
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 185 VAIVGKPNVGKSTLINSL 202
V +VG PN GKSTLI+++
Sbjct: 161 VGLVGLPNAGKSTLISAV 178
>gnl|CDD|202547 pfam03129, HGTP_anticodon, Anticodon binding domain. This domain is
found in histidyl, glycyl, threonyl and prolyl tRNA
synthetases it is probably the anticodon binding domain.
Length = 93
Score = 49.1 bits (118), Expect = 3e-07
Identities = 22/100 (22%), Positives = 44/100 (44%), Gaps = 10/100 (10%)
Query: 1141 QCDIYIVHVGKEAELKAFVLSENLRTLGLKVILNCVFNNIHESFKSQMKRANASNANFAA 1200
Q + + E E A L+E LR G++V L+ +ES + + A+ F
Sbjct: 1 QVVVIPLGEKDELEDYAQKLAEELREAGIRVELDDR----NESLGKKFRDADLIGIPFRL 56
Query: 1201 IIGENEIINNTLIIKDLRNKYEDPTLKQISISFKDAENYF 1240
++GE E+ N T+ ++D ++ ++S ++
Sbjct: 57 VVGEKELENGTVTVRDRDTG------EKETVSLEELVEKL 90
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 50.5 bits (122), Expect = 5e-07
Identities = 48/181 (26%), Positives = 78/181 (43%), Gaps = 42/181 (23%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYP--------GLTRDRHYGEGYIGKKSFIIID-- 56
LVG PN GKSTL + ++N++ +A+YP G+ R +SF+I D
Sbjct: 5 LVGLPNAGKSTLLSAISNAKPK-IADYPFTTLVPNLGVVRVD-------DGRSFVIADIP 56
Query: 57 ---TGGFEPEVKKGIMHEMTKQTKQAIIE-SDIIIFIVD--GRQGLVEQDKLITNFLRK- 109
G E KG+ H + IE + +++ ++D G VE + I N L
Sbjct: 57 GLIEGASE---GKGLGHRFLRH-----IERTRVLLHVIDLSGEDDPVEDYETIRNELEAY 108
Query: 110 ----SGQPIVLVINK-----SENINSSISLDFYELGIGNPHIISALYGNGIKNFLENILT 160
+ +P ++V+NK +E + EL ISAL G G+ L+ +
Sbjct: 109 NPGLAEKPRIVVLNKIDLLDAEERFEKLKELLKELKGKKVFPISALTGEGLDELLKKLAK 168
Query: 161 I 161
+
Sbjct: 169 L 169
Score = 37.8 bits (89), Expect = 0.012
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 185 VAIVGKPNVGKSTLINSL 202
V +VG PN GKSTL++++
Sbjct: 3 VGLVGLPNAGKSTLLSAI 20
>gnl|CDD|206683 cd01896, DRG, Developmentally Regulated GTP-binding protein (DRG).
The developmentally regulated GTP-binding protein (DRG)
subfamily is an uncharacterized member of the Obg
family, an evolutionary branch of GTPase superfamily
proteins. GTPases act as molecular switches regulating
diverse cellular processes. DRG2 and DRG1 comprise the
DRG subfamily in eukaryotes. In view of their widespread
expression in various tissues and high conservation
among distantly related species in eukaryotes and
archaea, DRG proteins may regulate fundamental cellular
processes. It is proposed that the DRG subfamily
proteins play their physiological roles through RNA
binding.
Length = 233
Score = 51.4 bits (124), Expect = 7e-07
Identities = 34/119 (28%), Positives = 60/119 (50%), Gaps = 22/119 (18%)
Query: 183 IKVAIVGKPNVGKSTLINSLLG-ENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGI- 240
+VA+VG P+VGKSTL++ L ++ V Y TT + + EY K L+D GI
Sbjct: 1 ARVALVGFPSVGKSTLLSKLTNTKSEVAAY--EFTTLTCVPGVMEYKGAKIQLLDLPGII 58
Query: 241 ------RRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESG 293
+ R + +VI +V +T A++++++LDA + ++I + + G
Sbjct: 59 EGASDGKGRGR--QVI---AVART------ADLILIVLDATKPEGQREI-LERELEGVG 105
Score = 39.1 bits (92), Expect = 0.008
Identities = 16/29 (55%), Positives = 21/29 (72%), Gaps = 1/29 (3%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYP 34
LVG P+VGKSTL ++LTN+ + VA Y
Sbjct: 4 ALVGFPSVGKSTLLSKLTNT-KSEVAAYE 31
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 52.7 bits (127), Expect = 7e-07
Identities = 36/115 (31%), Positives = 60/115 (52%), Gaps = 18/115 (15%)
Query: 185 VAIVGKPNVGKSTLINSLLG-ENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGI--- 240
VA+VG P+VGKSTL+N L ++ V Y P TT + + + EY + L+D GI
Sbjct: 66 VALVGFPSVGKSTLLNKLTNTKSEVADY--PFTTLEPVPGMLEYKGAQIQLLDLPGIIEG 123
Query: 241 --RRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESG 293
R + +V+ SV + A+++I++LD ++ +DI I + + G
Sbjct: 124 ASSGRGRGRQVL---SVARN------ADLIIIVLDVFEDPHHRDI-IERELEDVG 168
Score = 41.5 bits (98), Expect = 0.002
Identities = 30/102 (29%), Positives = 46/102 (45%), Gaps = 13/102 (12%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDR-----HYGEGYIGKKSFIIIDTGGF 60
LVG P+VGKSTL N+LTN++ VA+YP T + Y I ++D G
Sbjct: 67 ALVGFPSVGKSTLLNKLTNTKSE-VADYPFTTLEPVPGMLEYKGAQIQ-----LLDLPGI 120
Query: 61 EPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKL 102
G +Q +D+II ++D + +D +
Sbjct: 121 IEGASSG--RGRGRQVLSVARNADLIIIVLDVFEDPHHRDII 160
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like
protein)-like YfjP subfamily includes several
uncharacterized bacterial GTPases that are similar to
Era. They generally show sequence conservation in the
region between the Walker A and B motifs (G1 and G3 box
motifs), to the exclusion of other GTPases. Era is
characterized by a distinct derivative of the KH domain
(the pseudo-KH domain) which is located C-terminal to
the GTPase domain.
Length = 140
Score = 48.5 bits (116), Expect = 1e-06
Identities = 30/123 (24%), Positives = 55/123 (44%), Gaps = 5/123 (4%)
Query: 186 AIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRRRNK 245
++GK GKS+L N+L G D TTR + +++ +L+D G+ R +
Sbjct: 1 GLMGKTGAGKSSLCNALFGTEVAAVGDRRPTTRAAQAYVWQTGGDGLVLLDLPGVGERGR 60
Query: 246 TFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRS-LIVCVNKWD 304
E+ + + EA++V+ LLDA A D + + L+ +N+ D
Sbjct: 61 RDREYEELY----RRLLPEADLVLWLLDADDRALAADHDFYLLPLAGHDAPLLFVLNQVD 116
Query: 305 SII 307
++
Sbjct: 117 PVL 119
Score = 44.3 bits (105), Expect = 5e-05
Identities = 25/121 (20%), Positives = 52/121 (42%), Gaps = 5/121 (4%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGFEPEVK 65
L+G+ GKS+L N L + A V + TR G +++D G
Sbjct: 1 GLMGKTGAGKSSLCNALFGTEVAAVGDRRPTTRAAQAYVWQTGGDGLVLLDLPGVGE--- 57
Query: 66 KGIMH-EMTKQTKQAIIESDIIIFIVDG-RQGLVEQDKLITNFLRKSGQPIVLVINKSEN 123
+G E + ++ + E+D++++++D + L L P++ V+N+ +
Sbjct: 58 RGRRDREYEELYRRLLPEADLVLWLLDADDRALAADHDFYLLPLAGHDAPLLFVLNQVDP 117
Query: 124 I 124
+
Sbjct: 118 V 118
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 51.4 bits (124), Expect = 2e-06
Identities = 23/47 (48%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 1 MKPVLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYI 47
M + +VG PNVGKSTLFN LT + A +ANYP T + + G Y+
Sbjct: 1 MSLKIGIVGLPNVGKSTLFNALTKA-GAEIANYPFCTIEPNVGVVYV 46
Score = 41.8 bits (99), Expect = 0.002
Identities = 14/20 (70%), Positives = 17/20 (85%)
Query: 183 IKVAIVGKPNVGKSTLINSL 202
+K+ IVG PNVGKSTL N+L
Sbjct: 3 LKIGIVGLPNVGKSTLFNAL 22
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 51.0 bits (123), Expect = 2e-06
Identities = 49/150 (32%), Positives = 72/150 (48%), Gaps = 43/150 (28%)
Query: 110 SGQPIVLVINKSE----NINSSISLDF-----YELGIGNP---HIISALYGNGIKNFLEN 157
P++LV NK++ ++ + ++ ELG+ P +ISA G+GI LE
Sbjct: 95 GNNPVLLVGNKADLLPKSVKKNKVKNWLRQEAKELGL-RPVDVVLISAQKGHGIDELLE- 152
Query: 158 ILTIELPYKKFFKKKEFTNIHSIEYIKVAIVGKPNVGKSTLINSLL----GENRVITYDT 213
IE K+ + ++ V +VG NVGKSTLIN ++ GE VIT T
Sbjct: 153 --AIE----KYREGRD-----------VYVVGVTNVGKSTLINRIIKEITGEKDVIT--T 193
Query: 214 ---PGTTRDSIKSLFEYNNKKYILIDTAGI 240
PGTT D I+ + + + L DT GI
Sbjct: 194 SRFPGTTLDKIEIPLD--DGSF-LYDTPGI 220
Score = 31.4 bits (72), Expect = 3.1
Identities = 18/44 (40%), Positives = 21/44 (47%), Gaps = 17/44 (38%)
Query: 8 VGRPNVGKSTLFNRL-----------TNSRDALVANYPGLTRDR 40
VG NVGKSTL NR+ T SR +PG T D+
Sbjct: 166 VGVTNVGKSTLINRIIKEITGEKDVITTSR------FPGTTLDK 203
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 50.8 bits (123), Expect = 3e-06
Identities = 19/27 (70%), Positives = 20/27 (74%), Gaps = 1/27 (3%)
Query: 8 VGRPNVGKSTLFNRLTNSRDALVANYP 34
VG PNVGKSTLFN LT + A ANYP
Sbjct: 8 VGLPNVGKSTLFNALTKA-GAEAANYP 33
Score = 38.9 bits (92), Expect = 0.016
Identities = 14/20 (70%), Positives = 16/20 (80%)
Query: 183 IKVAIVGKPNVGKSTLINSL 202
+K IVG PNVGKSTL N+L
Sbjct: 3 LKCGIVGLPNVGKSTLFNAL 22
>gnl|CDD|206686 cd01899, Ygr210, Ygr210 GTPase. Ygr210 is a member of Obg-like
family and present in archaea and fungi. They are
characterized by a distinct glycine-rich motif
immediately following the Walker B motif. The Ygr210
and YyaF/YchF subfamilies appear to form one major
branch of the Obg-like family. Among eukaryotes, the
Ygr210 subfamily is represented only in fungi. These
fungal proteins form a tight cluster with their
archaeal orthologs, which suggests the possibility of
horizontal transfer from archaea to fungi.
Length = 318
Score = 50.3 bits (121), Expect = 3e-06
Identities = 23/41 (56%), Positives = 28/41 (68%), Gaps = 1/41 (2%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYI 47
LVG+PNVGKST FN T + D +ANYP T D + G GY+
Sbjct: 3 LVGKPNVGKSTFFNAATLA-DVEIANYPFTTIDPNVGVGYV 42
Score = 36.8 bits (86), Expect = 0.059
Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 3/34 (8%)
Query: 185 VAIVGKPNVGKSTLINSL-LGENRVITYDTPGTT 217
+ +VGKPNVGKST N+ L + + Y P TT
Sbjct: 1 IGLVGKPNVGKSTFFNAATLADVEIANY--PFTT 32
>gnl|CDD|206753 cd04178, Nucleostemin_like, A circularly permuted subfamily of the
Ras GTPases. Nucleostemin (NS) is a nucleolar protein
that functions as a regulator of cell growth and
proliferation in stem cells and in several types of
cancer cells, but is not expressed in the differentiated
cells of most mammalian adult tissues. NS shuttles
between the nucleolus and nucleoplasm bidirectionally at
a rate that is fast and independent of cell type.
Lowering GTP levels decreases the nucleolar retention of
NS, and expression of NS is abruptly down-regulated
during differentiation prior to terminal cell division.
Found only in eukaryotes, NS consists of an N-terminal
basic domain, a coiled-coil domain, a GTP-binding
domain, an intermediate domain, and a C-terminal acidic
domain. Experimental evidence indicates that NS uses its
GTP-binding property as a molecular switch to control
the transition between the nucleolus and nucleoplasm,
and this process involves interaction between the basic,
GTP-binding, and intermediate domains of the protein.
Length = 171
Score = 48.0 bits (115), Expect = 4e-06
Identities = 25/59 (42%), Positives = 34/59 (57%), Gaps = 5/59 (8%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYN-NKKYILIDTAGI 240
I V +VG PNVGKS++INSL TPG T KS+ E + +K L+D+ G+
Sbjct: 117 ITVGVVGYPNVGKSSVINSLKRSRACNVGATPGVT----KSMQEVHLDKHVKLLDSPGV 171
Score = 41.4 bits (98), Expect = 8e-04
Identities = 16/31 (51%), Positives = 20/31 (64%)
Query: 8 VGRPNVGKSTLFNRLTNSRDALVANYPGLTR 38
VG PNVGKS++ N L SR V PG+T+
Sbjct: 122 VGYPNVGKSSVINSLKRSRACNVGATPGVTK 152
>gnl|CDD|206687 cd01900, YchF, YchF GTPase. YchF is a member of the Obg family,
which includes four other subfamilies of GTPases: Obg,
DRG, Ygr210, and NOG1. Obg is an essential gene that is
involved in DNA replication in C. crescentus and
Streptomyces griseus and is associated with the
ribosome. Several members of the family, including
YchF, possess the TGS domain related to the RNA-binding
proteins. Experimental data and genomic analysis
suggest that YchF may be part of a nucleoprotein
complex and may function as a GTP-dependent
translational factor.
Length = 274
Score = 49.4 bits (119), Expect = 4e-06
Identities = 20/27 (74%), Positives = 21/27 (77%), Gaps = 1/27 (3%)
Query: 8 VGRPNVGKSTLFNRLTNSRDALVANYP 34
VG PNVGKSTLFN LT S +A ANYP
Sbjct: 4 VGLPNVGKSTLFNALTKS-NAEAANYP 29
Score = 34.7 bits (81), Expect = 0.22
Identities = 13/16 (81%), Positives = 14/16 (87%)
Query: 187 IVGKPNVGKSTLINSL 202
IVG PNVGKSTL N+L
Sbjct: 3 IVGLPNVGKSTLFNAL 18
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 49.0 bits (118), Expect = 9e-06
Identities = 44/179 (24%), Positives = 79/179 (44%), Gaps = 37/179 (20%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYP--------GLTRDRHYGEGYIGKKSFIIIDTG 58
LVG PN GKSTL + ++ ++ +A+YP G+ R +G +SF+I D
Sbjct: 162 LVGLPNAGKSTLISAVSAAK-PKIADYPFTTLVPNLGVVR---VDDG----RSFVIADIP 213
Query: 59 GFEPEVK--KGIMHEMTKQTKQAIIE-SDIIIFIVDG----RQGLVEQDKLITNFLRK-- 109
G G+ H K IE + +++ ++D +E ++I N L+K
Sbjct: 214 GLIEGASEGAGLGHRFLKH-----IERTRVLLHLIDISPEDGSDPIEDYEIIRNELKKYS 268
Query: 110 ---SGQPIVLVINKSENINSS----ISLDFYELGIGNPHIISALYGNGIKNFLENILTI 161
+ +P ++V+NK + ++ + + E ISAL G G+ L + +
Sbjct: 269 PELAEKPRIVVLNKIDLLDEEELEELLKELKEALGKPVFPISALTGEGLDELLYALAEL 327
Score = 37.8 bits (89), Expect = 0.032
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 185 VAIVGKPNVGKSTLINSL 202
V +VG PN GKSTLI+++
Sbjct: 160 VGLVGLPNAGKSTLISAV 177
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 49.0 bits (118), Expect = 1e-05
Identities = 22/44 (50%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKK 50
LVG+PNVGKST FN T + D +ANYP T D + G Y+ +
Sbjct: 6 LVGKPNVGKSTFFNAATLA-DVEIANYPFTTIDPNVGVAYVRVE 48
Score = 38.3 bits (90), Expect = 0.021
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 183 IKVAIVGKPNVGKSTLINS 201
I + +VGKPNVGKST N+
Sbjct: 2 ITIGLVGKPNVGKSTFFNA 20
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 46.4 bits (111), Expect = 2e-05
Identities = 46/145 (31%), Positives = 64/145 (44%), Gaps = 38/145 (26%)
Query: 1 MKPVLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRD-RHYGEGYIGKKSFIIIDTGG 59
KP +V VGR NVGKSTL LT + V PG+TR HY FI+ D G
Sbjct: 8 RKPEIVFVGRSNVGKSTLVRELT-GKKVRVGKRPGVTRKPNHY-----DWGDFILTDLPG 61
Query: 60 FEPEVKKGIMHEMTKQTKQAIIESDIIIFI-------------VDG-----------RQG 95
F G M + K+ Q I+ +I+ +I VDG +G
Sbjct: 62 F------GFMSGVPKE-VQEKIKDEIVRYIEDNADRILAAVLVVDGKSFIEIIERWEGRG 114
Query: 96 LVEQDKLITNFLRKSGQPIVLVINK 120
+ D + +FLR+ G P ++ +NK
Sbjct: 115 EIPIDVEMFDFLRELGIPPIVAVNK 139
Score = 41.4 bits (98), Expect = 0.001
Identities = 51/196 (26%), Positives = 78/196 (39%), Gaps = 44/196 (22%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAG--- 239
++ VG+ NVGKSTL+ L G+ +V PG TR Y+ +IL D G
Sbjct: 10 PEIVFVGRSNVGKSTLVRELTGK-KVRVGKRPGVTRKPN----HYDWGDFILTDLPGFGF 64
Query: 240 -------IRRRNKTFEV--IEKFSVIKTLKSILEANVVILLLDAQQNIS----------- 279
++ + K V IE + IL A +L++D + I
Sbjct: 65 MSGVPKEVQEKIKDEIVRYIEDNA-----DRILAA---VLVVDGKSFIEIIERWEGRGEI 116
Query: 280 AQDINIANFIYESGRSLIVCVNKWDSIIHNQRKIIKNNIKKKLNFLS-----FAMFNFIS 334
D+ + +F+ E G IV VNK D I + + + I ++L + IS
Sbjct: 117 PIDVEMFDFLRELGIPPIVAVNKMDKIKNRDEVL--DEIAERLGLYPPWRQWQDIIAPIS 174
Query: 335 AIKLNNINSFMESINH 350
A K I E+I
Sbjct: 175 A-KKGGIEELKEAIRK 189
>gnl|CDD|237098 PRK12421, PRK12421, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 392
Score = 47.7 bits (114), Expect = 3e-05
Identities = 84/336 (25%), Positives = 138/336 (41%), Gaps = 58/336 (17%)
Query: 866 LSGEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLI-YDGPKRLWYSGPMF 924
L+G D+ K + + ID+L+G + +R + T V R I+ +L+ +G RL Y+G +
Sbjct: 55 LTGAGQDL-KLQTFKLIDQLSGRLMGVRADITPQVAR--IDAHLLNREGVARLCYAGSVL 111
Query: 925 RHERPQ-YGRYRQFYQIGVEAIGFPGPDIDAELIIMCSRLWKNLNLKNICLELNSIGNF- 982
H PQ R Q+G E G G + D E+I + L +N + + L+L +G F
Sbjct: 112 -HTLPQGLFGSRTPLQLGAELYGHAGIEADLEIIRLMLGLLRNAGVPALHLDLGHVGIFR 170
Query: 983 ---------NERKKYCIDLINYIKKHKDS-KWFC------EDIKHSLY----LNS-LRVL 1021
E ++ DL +K C D++ Y LN L L
Sbjct: 171 RLAELAGLSPEEEEELFDL--LQRKALPELAEVCQNLGVGSDLRRMFYALARLNGGLEAL 228
Query: 1022 DSKNLIIREILINAP----KLLDYLEKDSLDHFYGIQKILNYNNISYKINTKLVRGMDYY 1077
D +L + LD L K H ++ +S + +L RG Y+
Sbjct: 229 DRA----LSVLALQDAAIRQALDEL-KTLAAH---LKNRWPELPVSIDL-AEL-RGYHYH 278
Query: 1078 NRTVFEWTTDKLGSQNSICGGGRYDFLIKKFSNKFVPASGFAIGIERLIELIKKININHN 1137
VF G ++ GGRYD I + + PA+GF++ ++ L+ L
Sbjct: 279 TGLVFAAYIP--GRGQALARGGRYDG-IGEAFGRARPATGFSMDLKELLALQ-------- 327
Query: 1138 FSHQCDIYIVHV-GKEAELKAFVLSENLRTLGLKVI 1172
F + I+ G + +L A + LR G +V+
Sbjct: 328 FLEEEAGAILAPWGDDPDLLAAI--AELRQQGERVV 361
>gnl|CDD|100105 cd01335, Radical_SAM, Radical SAM superfamily. Enzymes of this
family generate radicals by combining a 4Fe-4S cluster
and S-adenosylmethionine (SAM) in close proximity. They
are characterized by a conserved CxxxCxxC motif, which
coordinates the conserved iron-sulfur cluster.
Mechanistically, they share the transfer of a single
electron from the iron-sulfur cluster to SAM, which
leads to its reductive cleavage to methionine and a
5'-deoxyadenosyl radical, which, in turn, abstracts a
hydrogen from the appropriately positioned carbon atom.
Depending on the enzyme, SAM is consumed during this
process or it is restored and reused. Radical SAM
enzymes catalyze steps in metabolism, DNA repair, the
biosynthesis of vitamins and coenzymes, and the
biosynthesis of many antibiotics. Examples are biotin
synthase (BioB), lipoyl synthase (LipA), pyruvate
formate-lyase (PFL), coproporphyrinogen oxidase (HemN),
lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide
reductase (ARR), and MoaA, an enzyme of the
biosynthesis of molybdopterin.
Length = 204
Score = 46.2 bits (109), Expect = 3e-05
Identities = 33/161 (20%), Positives = 56/161 (34%), Gaps = 25/161 (15%)
Query: 625 GCAINCIFCSTGRQ-GFVRNLTVGEIIGQLWVTEFKLRREKNIKINSQGKRQITNIVMMG 683
GC +NC FCS G V E K R + +V++
Sbjct: 6 GCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEAKERGVE--------------VVILT 51
Query: 684 MGEPLLNYKSTIGALKLILSDHAYGLSRRHVILSTSGIIPM---IDKLAQECPVELAVSL 740
GEPLL L +L L + + T+G + + +L + + VSL
Sbjct: 52 GGEPLLYP-----ELAELLRRLKKELPGFEISIETNGTLLTEELLKELKELGLDGVGVSL 106
Query: 741 HASNNNLRNKLV--PISKKYPLKELILACHRYITYSPRHMI 779
+ + + +K+ S K L+ L + S ++
Sbjct: 107 DSGDEEVADKIRGSGESFKERLEALKELREAGLGLSTTLLV 147
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 47.2 bits (113), Expect = 3e-05
Identities = 42/177 (23%), Positives = 76/177 (42%), Gaps = 31/177 (17%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYI-GKKSFIIIDTGGFEPEVK 65
LVG PN GKSTL + ++ ++ +A+YP T + G + G +SF++ D G ++
Sbjct: 164 LVGLPNAGKSTLLSAVSAAKPK-IADYPFTTLVPNLGVVRVDGGESFVVADIPGL---IE 219
Query: 66 -----KGIMHEMTKQTKQAIIE-SDIIIFIVDG----RQGLVEQDKLITNFLRKSGQ--- 112
G+ + IE + +++ ++D + +E + I N L K
Sbjct: 220 GASEGVGLGLRFLRH-----IERTRVLLHVIDLSPIDGRDPIEDYQTIRNELEKYSPKLA 274
Query: 113 --PIVLVINKS------ENINSSISLDFYELGIGNPHIISALYGNGIKNFLENILTI 161
P ++V+NK E + LG ++ISAL G+ L + +
Sbjct: 275 EKPRIVVLNKIDLPLDEEELEELKKALAEALGWEVFYLISALTREGLDELLRALAEL 331
Score = 35.6 bits (83), Expect = 0.13
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 185 VAIVGKPNVGKSTLINSL 202
V +VG PN GKSTL++++
Sbjct: 162 VGLVGLPNAGKSTLLSAV 179
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 45.7 bits (108), Expect = 4e-05
Identities = 30/124 (24%), Positives = 45/124 (36%), Gaps = 15/124 (12%)
Query: 5 LVLVGRPNVGKSTLFNRLTNS------RDALVANYPGLTRDRHYGEGYIGKKSFIIIDTG 58
+V++G VGK+TL NRL + P T E Y + DT
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTI-----EPYRRNIKLQLWDTA 62
Query: 59 GFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVI 118
G E + + E + +I D + + L E+ L PI+LV
Sbjct: 63 GQ--EEYRSLRPEYYRGANGILIVYDSTLR--ESSDELTEEWLEELRELAPDDVPILLVG 118
Query: 119 NKSE 122
NK +
Sbjct: 119 NKID 122
Score = 42.3 bits (99), Expect = 6e-04
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNK-KYILIDTAGIR 241
K+ ++G VGK+TL+N L+G+ Y D K++ Y K L DTAG
Sbjct: 6 FKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQE 65
Query: 242 R 242
Sbjct: 66 E 66
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 45.2 bits (108), Expect = 4e-05
Identities = 39/188 (20%), Positives = 72/188 (38%), Gaps = 39/188 (20%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRD------------SIKS---LFEYNN 229
+ I+G + GK+TL ++LL I+ ++ R +IK FE
Sbjct: 6 IGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVSFETKK 65
Query: 230 KKYILIDTAGIRRRNKTFEVIEKFS--VIKTLKSILEANVVILLLDAQQNISAQDINIAN 287
+ +IDT G F+ +I+ A+ IL++DA + + Q
Sbjct: 66 RLINIIDTPG----------HVDFTKEMIRGASQ---ADGAILVVDAVEGVMPQTREHLL 112
Query: 288 FIYESGRSLIVCVNKWDSIIHNQRKIIKNNIKKKLNFLSFAMFN-------FISAIKLNN 340
G +IV +NK D + + + + I ++ L F SA+
Sbjct: 113 LAKTLGVPIIVFINKIDRVDDAELEEVVEEISRE--LLEKYGFGGETVPVVPGSALTGEG 170
Query: 341 INSFMESI 348
I+ +E++
Sbjct: 171 IDELLEAL 178
Score = 44.0 bits (105), Expect = 1e-04
Identities = 35/125 (28%), Positives = 50/125 (40%), Gaps = 22/125 (17%)
Query: 49 KKSFIIIDTGGFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLR 108
K+ IIDT G K EM + QA D I +VD +G++ Q + +
Sbjct: 65 KRLINIIDTPGHVDFTK-----EMIRGASQA----DGAILVVDAVEGVMPQTREHLLLAK 115
Query: 109 KSGQPIVLVINK------------SENINSSISLDFYELGIGNPHI-ISALYGNGIKNFL 155
G PI++ INK E I+ + + G P + SAL G GI L
Sbjct: 116 TLGVPIIVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGSALTGEGIDELL 175
Query: 156 ENILT 160
E +
Sbjct: 176 EALDL 180
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 45.6 bits (108), Expect = 8e-05
Identities = 40/213 (18%), Positives = 73/213 (34%), Gaps = 42/213 (19%)
Query: 181 EYIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGI 240
E + V ++G GKS+LIN+L T + + Y+ + +L DT G+
Sbjct: 38 EPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLSYDGENLVLWDTPGL 97
Query: 241 ---RRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESG--RS 295
+ ++ L + ++V+ L+ A D + + G +
Sbjct: 98 GDGKDKDAEHRQ----LYRDYL---PKLDLVLWLIKADDRALGTDEDFLRDVIILGLDKR 150
Query: 296 LIVCVNK---------WDSIIHNQRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFME 346
++ V + WDS H IK I++K A+ +
Sbjct: 151 VLFVVTQADRAEPGREWDSAGHQPSPAIKQFIEEKAE----ALGRLF------------Q 194
Query: 347 SINHVYDSSII---HLSTSRITRALISAIKNHP 376
+ V S L + RALI+A+
Sbjct: 195 EVKPVVAVSGRLPWGLKE--LVRALITALPVEA 225
Score = 42.5 bits (100), Expect = 0.001
Identities = 23/124 (18%), Positives = 51/124 (41%), Gaps = 5/124 (4%)
Query: 2 KPVLVL-VGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGF 60
+PV VL +G GKS+L N L V+ T ++ ++ DT G
Sbjct: 38 EPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLSYDGENLVLWDTPGL 97
Query: 61 EPEVKKGIMHEMTKQTKQAIIESDIIIFIVDG--RQGLVEQDKLITNFLRKSGQPIVLVI 118
K H + + + + D++++++ R ++D L + + ++ V+
Sbjct: 98 GDGKDKDAEHR--QLYRDYLPKLDLVLWLIKADDRALGTDEDFLRDVIILGLDKRVLFVV 155
Query: 119 NKSE 122
+++
Sbjct: 156 TQAD 159
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 46.2 bits (110), Expect = 1e-04
Identities = 21/45 (46%), Positives = 31/45 (68%), Gaps = 2/45 (4%)
Query: 1 MKPVLV-LVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGE 44
MK + + L+G PN GK+TLFN+LT +R V N+ G+T +R G+
Sbjct: 1 MKKLTIGLIGNPNSGKTTLFNQLTGARQR-VGNWAGVTVERKEGQ 44
>gnl|CDD|206729 cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP
sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN,
together with protein CysD, form the ATP sulfurylase
(ATPS) complex in some bacteria and lower eukaryotes.
ATPS catalyzes the production of ATP sulfurylase (APS)
and pyrophosphate (PPi) from ATP and sulfate. CysD,
which catalyzes ATP hydrolysis, is a member of the ATP
pyrophosphatase (ATP PPase) family. CysN hydrolysis of
GTP is required for CysD hydrolysis of ATP; however,
CysN hydrolysis of GTP is not dependent on CysD
hydrolysis of ATP. CysN is an example of lateral gene
transfer followed by acquisition of new function. In
many organisms, an ATPS exists which is not
GTP-dependent and shares no sequence or structural
similarity to CysN.
Length = 209
Score = 44.5 bits (106), Expect = 1e-04
Identities = 33/120 (27%), Positives = 52/120 (43%), Gaps = 28/120 (23%)
Query: 48 GKKSFIIIDTGGFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDK---LIT 104
K+ FII DT G E + T+ +D+ I +VD R+G++EQ + I
Sbjct: 76 PKRKFIIADTPGHE---------QYTRNMVTGASTADLAILLVDARKGVLEQTRRHSYIA 126
Query: 105 NFLRKSGQP-IVLVINK------SENINSSISLDFYEL--GIGNPHI----ISALYGNGI 151
+ L G +V+ +NK E + I D+ +G I ISAL G+ +
Sbjct: 127 SLL---GIRHVVVAVNKMDLVDYDEEVFEEIKADYLAFAASLGIEDITFIPISALEGDNV 183
Score = 32.2 bits (74), Expect = 1.4
Identities = 44/204 (21%), Positives = 72/204 (35%), Gaps = 67/204 (32%)
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVITYDT------------------------------ 213
+ G + GKSTLI LL +++ I D
Sbjct: 1 RFITCGSVDDGKSTLIGRLLYDSKSIFEDQLAALERSKSSGTQGEKLDLALLVDGLQAER 60
Query: 214 -PGTTRDSIKSLFEYNNKKYILIDTAGIRR--RNKTFEVIEKFSVIKTLKSILEANVVIL 270
G T D F +K+I+ DT G + RN + A++ IL
Sbjct: 61 EQGITIDVAYRYFSTPKRKFIIADTPGHEQYTRN-------------MVTGASTADLAIL 107
Query: 271 LLDAQQNISAQD---------INIANFIYESGRSLIVCVNKWDSIIHNQRKI--IKNNIK 319
L+DA++ + Q + I R ++V VNK D + +++ IK +
Sbjct: 108 LVDARKGVLEQTRRHSYIASLLGI--------RHVVVAVNKMDLVDYDEEVFEEIKADYL 159
Query: 320 KKLNFLSFAMFNFI--SAIKLNNI 341
L FI SA++ +N+
Sbjct: 160 AFAASLGIEDITFIPISALEGDNV 183
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 45.7 bits (109), Expect = 1e-04
Identities = 26/65 (40%), Positives = 34/65 (52%), Gaps = 12/65 (18%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITY-----DTPG---TTRDSIKSLFEYNNKKYILID 236
VA++G VGKSTL+N+LLGE T D+ G TT + L +LID
Sbjct: 198 VALLGSSGVGKSTLVNALLGEEVQKTGAVREDDSKGRHTTTHRELHPLPS----GGLLID 253
Query: 237 TAGIR 241
T G+R
Sbjct: 254 TPGMR 258
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 44.3 bits (106), Expect = 1e-04
Identities = 46/158 (29%), Positives = 64/158 (40%), Gaps = 48/158 (30%)
Query: 102 LITNFL---RKSGQPIVLVINKSENINSSIS---LDFYE-LGIGNPHIISALYGNGIKNF 154
L+ +L SG V+V+NK++ ++ L+ YE LG +SA G G+
Sbjct: 21 LLDRYLVAAEASGIEPVIVLNKADLVDDEELEELLEIYEKLGY-PVLAVSAKTGEGLD-- 77
Query: 155 LENILTIELPYKKFFKKKEFTNIHSIEYIKVAIVGKPNVGKSTLINSLLGENRVITYDTP 214
EL ++ K K T +VG+ VGKSTL+N+LL E + T
Sbjct: 78 -------EL--RELLKGK--T---------SVLVGQSGVGKSTLLNALLPELVLAT---- 113
Query: 215 G-----------TTRDSIKSLFEYNNKKYILIDTAGIR 241
G TT LF I IDT G R
Sbjct: 114 GEISEKLGRGRHTTTHR--ELFPLPGGGLI-IDTPGFR 148
>gnl|CDD|183411 PRK12293, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 281
Score = 44.2 bits (105), Expect = 2e-04
Identities = 67/262 (25%), Positives = 113/262 (43%), Gaps = 42/262 (16%)
Query: 875 KKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMFRHERPQYGRY 934
+KE+ F DE N +SLR + T V+R V + K+ +Y P+FR+
Sbjct: 57 EKELIRFSDEKN-HQISLRADSTLDVVRIVTKRLGRSTEHKKWFYIQPVFRYPS------ 109
Query: 935 RQFYQIGVEAIGFPGPDIDAELIIMCSRLWKNLNLKNICLELNSIGNFNERKKYCIDL-- 992
+ YQIG E IG D+ +E++ + + +++ L L+ I I N K L
Sbjct: 110 NEIYQIGAELIG--EEDL-SEILNIAAEIFEELELEPIL----QISNIKIPKLVAEILGL 162
Query: 993 -INYIKKHKDSKWFCEDIKHSLYLNSL-RVLDSKNLIIREILINAPKLLDYLEKDSLDHF 1050
I KK + K +++ +LN L R+ ++L E++ P + K+ L+
Sbjct: 163 DIEVFKKGQIEKLLAQNVP---WLNKLVRIKTLEDL--DEVIELVPDEI----KEELEKL 213
Query: 1051 YGIQKILNYNNISYKINTKLVRGMDYYNRTVFEWTTDKLGSQNSI-CGGGRYDFLIKKFS 1109
+ + + Y N+ I M YY+ F + NS GG Y
Sbjct: 214 KELAESIKYENLV--IAPLYYAKMRYYDDLFFRFFDG-----NSTLASGGNY-------E 259
Query: 1110 NKFVPASGFAIGIERLIELIKK 1131
+ +SGFA+ + LIE++ K
Sbjct: 260 IDGISSSGFALYTDNLIEILLK 281
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 41.2 bits (97), Expect = 4e-04
Identities = 18/100 (18%), Positives = 35/100 (35%), Gaps = 12/100 (12%)
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILI-DTAGIRR 242
KV ++G GKS+L++ L+G ++ +L + + I D G
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 243 RNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQD 282
+ K A+ ++L+ D S +
Sbjct: 61 LKFEHIIFMK-----------WADAILLVYDLTDRESLNE 89
Score = 36.2 bits (84), Expect = 0.019
Identities = 28/123 (22%), Positives = 45/123 (36%), Gaps = 16/123 (13%)
Query: 5 LVLVGRPNVGKSTLFNRL-TNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGFEPE 63
+V++G GKS+L ++L G T E I D GG E E
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGRE-E 60
Query: 64 VKKGIMHEMTKQTKQAIIESDIIIFIVDGRQG-----LVEQDKLITNFLRKSGQ-PIVLV 117
+K + M +D I+ + D + + N + G+ P++LV
Sbjct: 61 LKFEHIIFMKW--------ADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILV 112
Query: 118 INK 120
NK
Sbjct: 113 GNK 115
>gnl|CDD|213679 TIGR02034, CysN, sulfate adenylyltransferase, large subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. Homologous to this E.coli
activation pathway are nodPQH gene products found among
members of the Rhizobiaceae family. These gene products
have been shown to exhibit ATP sulfurase and APS kinase
activity, yet are involved in Nod factor sulfation, and
sulfation of other macromolecules. With members of the
Rhizobiaceae family, nodQ often appears as a fusion of
cysN (large subunit of ATP sulfurase) and cysC (APS
kinase) [Central intermediary metabolism, Sulfur
metabolism].
Length = 406
Score = 43.1 bits (102), Expect = 7e-04
Identities = 32/121 (26%), Positives = 55/121 (45%), Gaps = 28/121 (23%)
Query: 49 KKSFIIIDTGGFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDK---LITN 105
K+ FI+ DT G E + T+ +D+ + +VD R+G++EQ + I +
Sbjct: 79 KRKFIVADTPGHE---------QYTRNMATGASTADLAVLLVDARKGVLEQTRRHSYIAS 129
Query: 106 FLRKSG-QPIVLVINK------SENINSSISLDFYE----LGIGNPHII--SALYGNGIK 152
L G + +VL +NK E + +I D+ LG + I SAL G+ +
Sbjct: 130 LL---GIRHVVLAVNKMDLVDYDEEVFENIKKDYLAFAEQLGFRDVTFIPLSALKGDNVV 186
Query: 153 N 153
+
Sbjct: 187 S 187
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 42.2 bits (100), Expect = 0.001
Identities = 44/195 (22%), Positives = 69/195 (35%), Gaps = 69/195 (35%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYP--------GLTRDRHYGEGYIGKKSFIIIDTG 58
L+G PN GKST ++ ++ VA+YP G+ R +SF++ D
Sbjct: 164 LLGLPNAGKSTFIRAVSAAKPK-VADYPFTTLVPNLGVVRVDDE-------RSFVVADIP 215
Query: 59 GFEPEVKKGIMHEMTKQTKQAIIE--SD----------------IIIFIVDGRQG----L 96
G +IE S+ +++ ++D
Sbjct: 216 G--------------------LIEGASEGAGLGIRFLKHLERCRVLLHLIDIAPIDGSDP 255
Query: 97 VEQDKLITNFLRK-----SGQPIVLVINKS-----ENINSSISLDFYELGIGNPHI-ISA 145
VE ++I N L K + +P LV NK E LG P ISA
Sbjct: 256 VENARIIINELEKYSPKLAEKPRWLVFNKIDLLDEEEAEERAKAIVEALGWEGPVYLISA 315
Query: 146 LYGNGIKNFLENILT 160
G G+K +++T
Sbjct: 316 ASGLGVKELCWDLMT 330
Score = 31.8 bits (73), Expect = 2.7
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 185 VAIVGKPNVGKSTLINSL 202
V ++G PN GKST I ++
Sbjct: 162 VGLLGLPNAGKSTFIRAV 179
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 42.4 bits (101), Expect = 0.001
Identities = 15/28 (53%), Positives = 21/28 (75%), Gaps = 1/28 (3%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYP 34
LVG PNVGKSTL + ++N++ +ANY
Sbjct: 163 LVGFPNVGKSTLLSVVSNAKPK-IANYH 189
Score = 37.4 bits (88), Expect = 0.044
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 185 VAIVGKPNVGKSTLINSL 202
V +VG PNVGKSTL++ +
Sbjct: 161 VGLVGFPNVGKSTLLSVV 178
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 41.9 bits (99), Expect = 0.002
Identities = 16/35 (45%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRH 41
+VG PNVGKST FN L + N+P T D +
Sbjct: 26 IVGLPNVGKSTTFNALCKQQ-VPAENFPFCTIDPN 59
Score = 35.7 bits (83), Expect = 0.17
Identities = 13/19 (68%), Positives = 15/19 (78%)
Query: 184 KVAIVGKPNVGKSTLINSL 202
K+ IVG PNVGKST N+L
Sbjct: 23 KMGIVGLPNVGKSTTFNAL 41
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 41.1 bits (97), Expect = 0.003
Identities = 23/64 (35%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPG-------TTRDSIKSLFEYNNKKYILIDT 237
++G+ VGKSTLIN+LL E T + TT LF +I IDT
Sbjct: 167 TVLLGQSGVGKSTLINALLPELNQKTGEISEKLGRGRHTTTHV--ELFPLPGGGWI-IDT 223
Query: 238 AGIR 241
G R
Sbjct: 224 PGFR 227
Score = 32.6 bits (75), Expect = 1.1
Identities = 22/61 (36%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 4 VLVLVGRPNVGKSTLFNRLTNSRDALVANYPG-LTRDRH---YGEGYIGKKSFIIIDTGG 59
+ VL+G+ VGKSTL N L + L R RH + E + IIDT G
Sbjct: 166 ITVLLGQSGVGKSTLINALLPELNQKTGEISEKLGRGRHTTTHVELFPLPGGGWIIDTPG 225
Query: 60 F 60
F
Sbjct: 226 F 226
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 41.1 bits (97), Expect = 0.003
Identities = 40/209 (19%), Positives = 76/209 (36%), Gaps = 59/209 (28%)
Query: 181 EYIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSI-----------KSLFEYNN 229
++ + +G + GKSTL+ LL YD + ++ K F++
Sbjct: 6 PHLNLVFIGHVDAGKSTLVGRLL-------YDLGEIDKRTMEKLEKEAKELGKESFKF-- 56
Query: 230 KKYILIDTAGIRRRNKTFEV------IEKFS------------VIKTLKSILEANVVILL 271
++L T R R T +V +K++ V + +A+V +L+
Sbjct: 57 -AWVLDKTKEERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLV 115
Query: 272 LDAQQNISAQDINIANFIYESG--------RSLIVCVNKWDSIIHNQRKIIKNNIKKKLN 323
+DA+ + E + LIV VNK D + ++ + I +++
Sbjct: 116 VDARDGEFEAGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERF--EEIVSEVS 173
Query: 324 FLSFAMFNF---------ISAIKLNNINS 343
L M + IS K +N+
Sbjct: 174 KL-LKMVGYNPKDVPFIPISGFKGDNLTK 201
>gnl|CDD|206751 cd01858, NGP_1, A novel nucleolar GTP-binding protein, circularly
permuted subfamily of the Ras GTPases. Autoantigen
NGP-1 (Nucleolar G-protein gene 1) has been shown to
localize in the nucleolus and nucleolar organizers in
all cell types analyzed, which is indicative of a
function in ribosomal assembly. NGP-1 and its homologs
show a circular permutation of the GTPase signature
motifs so that the C-terminal strands 5, 6, and 7
(strand 6 contains the G4 box with NKXD motif) are
relocated to the N terminus.
Length = 157
Score = 39.2 bits (92), Expect = 0.003
Identities = 42/157 (26%), Positives = 70/157 (44%), Gaps = 47/157 (29%)
Query: 83 SDIIIFIVDGRQGLVEQDKLITNFLRKSGQP--IVLVINKSENINSSI--------SLDF 132
SD+II ++D R + + K + +LRK ++ V+NK + + + + S ++
Sbjct: 9 SDVIIQVLDARDPMGTRCKHVEKYLRKEKPHKHLIFVLNKCDLVPTWVTKRWVKVLSKEY 68
Query: 133 ----YELGIGNPHIISALYGNGIKNFLENILTIELPYKKFFKKKEFTNIHS-IEYIKVAI 187
+ I NP +G G L N+L ++F +HS + I V
Sbjct: 69 PTLAFHASITNP------FGKGA---LINLL------------RQFAKLHSDKKQISVGF 107
Query: 188 VGKPNVGKSTLINSL-----------LGENRVITYDT 213
+G PNVGKS++IN+L GE +V Y T
Sbjct: 108 IGYPNVGKSSVINTLRSKKVCKVAPIPGETKVWQYIT 144
Score = 33.0 bits (76), Expect = 0.42
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLTR 38
+G PNVGKS++ N L + + VA PG T+
Sbjct: 107 FIGYPNVGKSSVINTLRSKKVCKVAPIPGETK 138
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 39.1 bits (92), Expect = 0.004
Identities = 21/64 (32%), Positives = 28/64 (43%), Gaps = 10/64 (15%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPG-------TTRDSIKSLFEYNNKKYILIDT 237
+ G+ VGKSTL+N+LL E + T + TT LF + IDT
Sbjct: 38 SVLAGQSGVGKSTLLNALLPELDLRTGEISEKLGRGRHTTTHV--ELFPLPGGGLL-IDT 94
Query: 238 AGIR 241
G R
Sbjct: 95 PGFR 98
Score = 33.3 bits (77), Expect = 0.39
Identities = 23/68 (33%), Positives = 25/68 (36%), Gaps = 18/68 (26%)
Query: 4 VLVLVGRPNVGKSTLFNRLTNSRDALVANYPG-LTRDRH----------YGEGYIGKKSF 52
VL G+ VGKSTL N L D L R RH G G
Sbjct: 37 TSVLAGQSGVGKSTLLNALLPELDLRTGEISEKLGRGRHTTTHVELFPLPGGGL------ 90
Query: 53 IIIDTGGF 60
+IDT GF
Sbjct: 91 -LIDTPGF 97
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 39.6 bits (93), Expect = 0.005
Identities = 34/157 (21%), Positives = 65/157 (41%), Gaps = 39/157 (24%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLF------EYNNKKYILIDTA 238
V ++G + GK+ L L T +T SI+ KK L+D
Sbjct: 3 VLLLGPSDSGKTALFTKL-------TTGKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVP 55
Query: 239 GIRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDA---QQNISAQDINIANFIYE---- 291
G + + +++ LK+ L+A ++ ++D+ Q+NI +A F+Y+
Sbjct: 56 GHEKL--------RDKLLEYLKASLKA--IVFVVDSATFQKNIRD----VAEFLYDILTD 101
Query: 292 -----SGRSLIVCVNKWDSIIHNQRKIIKNNIKKKLN 323
+ +++ NK D K IK ++K++N
Sbjct: 102 LEKIKNKIPILIACNKQDLFTAKPAKKIKELLEKEIN 138
Score = 33.1 bits (76), Expect = 0.64
Identities = 29/129 (22%), Positives = 52/129 (40%), Gaps = 19/129 (14%)
Query: 3 PVLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLT-RDRHYGEGYIGKKSFIIIDTGGFE 61
P ++L+G + GK+ LF +LT + + + + K ++D G E
Sbjct: 1 PTVLLLGPSDSGKTALFTKLTT--GKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHE 58
Query: 62 PEVKKGIMHEMTKQTKQAIIESDIIIFIVDGR------QGLVEQ--DKLITNFLRKSGQP 113
K + E K + +A I+F+VD + + E D L K+ P
Sbjct: 59 KLRDKLL--EYLKASLKA------IVFVVDSATFQKNIRDVAEFLYDILTDLEKIKNKIP 110
Query: 114 IVLVINKSE 122
I++ NK +
Sbjct: 111 ILIACNKQD 119
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with the
signal sequence when it emerges from the ribosome. SRP54
of the signal recognition particle has a three-domain
structure: an N-terminal helical bundle domain, a GTPase
domain, and the M-domain that binds the 7s RNA and also
binds the signal sequence. The extreme C-terminal region
is glycine-rich and lower in complexity and poorly
conserved between species. The GTPase domain is
evolutionary related to P-loop NTPase domains found in a
variety of other proteins.
Length = 197
Score = 38.9 bits (92), Expect = 0.006
Identities = 19/92 (20%), Positives = 34/92 (36%), Gaps = 15/92 (16%)
Query: 203 LGENRVITYDTPGTTRDSIK------SLFEYNNKKYILIDTAGIRRRNKTFEVIEKFSVI 256
E + G D + L + +LIDTAG ++ +
Sbjct: 52 YAEILGVVPVAGGEGADPVAVAKDAVELAKARGYDVVLIDTAGRLHNDE-----NLMEEL 106
Query: 257 KTLKSILEANVVILLLDAQQNISAQD-INIAN 287
K +K +++ + V+L+ DA QD + A
Sbjct: 107 KKIKRVIKPDEVLLVSDATTG---QDAVEQAK 135
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 40.0 bits (94), Expect = 0.007
Identities = 34/120 (28%), Positives = 55/120 (45%), Gaps = 30/120 (25%)
Query: 49 KKSFIIIDTGGFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDK---LITN 105
K+ FII DT G E + T+ +D+ I +VD R+G++EQ + I +
Sbjct: 85 KRKFIIADTPGHE---------QYTRNMATGASTADLAILLVDARKGVLEQTRRHSFIAS 135
Query: 106 FL--RKSGQPIVLVINK------SENINSSISLDFYE----LGIGNPHII--SALYGNGI 151
L R +V+ +NK SE + +I D+ LG+ + I SAL G+ +
Sbjct: 136 LLGIRH----VVVAVNKMDLVDYSEEVFEAIVADYLAFAAQLGLKDVRFIPISALLGDNV 191
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 39.5 bits (93), Expect = 0.013
Identities = 27/87 (31%), Positives = 39/87 (44%), Gaps = 11/87 (12%)
Query: 84 DIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINKSENINSSISLDFYEL---GI--- 137
DI I +V G++ Q N + +G PIV+ INK + ++ EL G+
Sbjct: 80 DIAILVVAADDGVMPQTIEAINHAKAAGVPIVVAINKIDKPEANPDKVKQELQEYGLVPE 139
Query: 138 ---GNPHI--ISALYGNGIKNFLENIL 159
G+ +SA G GI LE IL
Sbjct: 140 EWGGDVIFVPVSAKTGEGIDELLELIL 166
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 39.3 bits (92), Expect = 0.013
Identities = 32/97 (32%), Positives = 47/97 (48%), Gaps = 17/97 (17%)
Query: 3 PVLVLVGRPNVGKSTLFNRLTNSR----DALVANY-PGLTRDRHYGEGYIGKKSFIIIDT 57
P + LVG N GKSTLFNR+T +R D L A P L R G ++ DT
Sbjct: 198 PTVSLVGYTNAGKSTLFNRITEARVYAADQLFATLDPTLRRIDVADVG-----ETVLADT 252
Query: 58 GGFEPEVKKGIMHEMT---KQTKQAIIESDIIIFIVD 91
GF + + H++ K T Q ++ +++ +VD
Sbjct: 253 VGF----IRHLPHDLVAAFKATLQETRQATLLLHVVD 285
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 39.4 bits (92), Expect = 0.014
Identities = 42/173 (24%), Positives = 77/173 (44%), Gaps = 30/173 (17%)
Query: 3 PVLVLVGRPNVGKSTLFNRLTNSRDALVAN--YPGLTRDRHYGEGYI---GKKSFIIIDT 57
PV+ ++G + GK++L + + R VA G+T+ H G ++ K +DT
Sbjct: 88 PVVTIMGHVDHGKTSLLDSI---RKTKVAQGEAGGITQ--HIGAYHVENEDGKMITFLDT 142
Query: 58 GGFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLV 117
G E M + + +DI++ +V G++ Q + + + PI++
Sbjct: 143 PGHEA------FTSMRARGAKV---TDIVVLVVAADDGVMPQTIEAISHAKAANVPIIVA 193
Query: 118 INKSENINSS---ISLDFYELGI-----GNPHI---ISALYGNGIKNFLENIL 159
INK + ++ + + E G+ G I +SAL G+GI L+ IL
Sbjct: 194 INKIDKPEANPDRVKQELSEYGLVPEDWGGDTIFVPVSALTGDGIDELLDMIL 246
Score = 30.5 bits (69), Expect = 6.8
Identities = 35/168 (20%), Positives = 74/168 (44%), Gaps = 16/168 (9%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYI-LIDTAGIRRR 243
V I+G + GK++L++S+ + +V + G T+ E + K I +DT G
Sbjct: 90 VTIMGHVDHGKTSLLDSIR-KTKVAQGEAGGITQHIGAYHVENEDGKMITFLDTPGH--- 145
Query: 244 NKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCVNKW 303
E F+ ++ + ++V+L++ A + Q I + + +IV +NK
Sbjct: 146 -------EAFTSMRA-RGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVPIIVAINKI 197
Query: 304 DSIIHNQRKIIKNNIKKKLNFLSFA---MFNFISAIKLNNINSFMESI 348
D N ++ + + L + +F +SA+ + I+ ++ I
Sbjct: 198 DKPEANPDRVKQELSEYGLVPEDWGGDTIFVPVSALTGDGIDELLDMI 245
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 37.3 bits (87), Expect = 0.023
Identities = 38/150 (25%), Positives = 59/150 (39%), Gaps = 28/150 (18%)
Query: 5 LVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGFEPEV 64
+V +G N GK+TL + L + R L + P T E IG F D GG
Sbjct: 22 IVFLGLDNAGKTTLLHMLKDDR--LAQHVP--TLHPTSEELTIGNVKFTTFDLGG----- 72
Query: 65 KKGIMHEMTKQT-KQAIIESDIIIFIVDG--RQGLVEQDKLITNFL---RKSGQPIVLVI 118
HE ++ K E D I+F+VD + E + + + L + PI+++
Sbjct: 73 -----HEQARRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVPILILG 127
Query: 119 NKS--------ENINSSISLDFYELGIGNP 140
NK E + ++ L G G
Sbjct: 128 NKIDKPGAVSEEELREALGLYGTTTGKGGV 157
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 160
Score = 35.6 bits (83), Expect = 0.052
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYIL--IDTAG 239
K+ ++G VGKS L + V YD P T DS + + + Y L +DTAG
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYD-P-TIEDSYRKQIVVDGETYTLDILDTAG 56
Score = 34.0 bits (79), Expect = 0.19
Identities = 33/129 (25%), Positives = 50/129 (38%), Gaps = 28/129 (21%)
Query: 5 LVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGY-----IGKKSFI--IIDT 57
LV++G VGKS L R + V Y D + Y + +++ I+DT
Sbjct: 2 LVVLGAGGVGKSALTIRFVSGE--FVEEY-----DPTIEDSYRKQIVVDGETYTLDILDT 54
Query: 58 GGFEPEVKKGIMHEMTKQTKQAIIESD--IIIFIVDGRQGLVEQDKLITNFLRKSGQ--- 112
G E + Q I D I+++ + R+ E + LR +
Sbjct: 55 AG---------QEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDV 105
Query: 113 PIVLVINKS 121
PIVLV NK
Sbjct: 106 PIVLVGNKC 114
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 36.3 bits (85), Expect = 0.057
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 20/66 (30%)
Query: 185 VAIVGKPNVGKSTLINSLLGE----------NRVITY--DTP----GTTRDSIKSLF--E 226
VAIVG GKS+L+++LLGE I Y P GT R++I LF
Sbjct: 34 VAIVGPVGSGKSSLLSALLGELEKLSGSVSVPGSIAYVSQEPWIQNGTIRENI--LFGKP 91
Query: 227 YNNKKY 232
++ ++Y
Sbjct: 92 FDEERY 97
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 35.3 bits (81), Expect = 0.065
Identities = 18/112 (16%), Positives = 43/112 (38%), Gaps = 11/112 (9%)
Query: 185 VAIVGKPNVGKSTLINSLL-------GENRVITYDTPGTTRDSIKSLFEY---NNKKYIL 234
V + G GK++L+ LL G+ + P +++ L +L
Sbjct: 27 VLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRELLRQLLRELAAELL 86
Query: 235 IDTAGIRRRNKTFEVIEKFSVIKTLKSILE-ANVVILLLDAQQNISAQDINI 285
+ + + +++ L+ +L A ++L+LD Q + +++
Sbjct: 87 LLREALLAALGAELIEGLQDLVELLERLLARARPLVLVLDDLQWADEESLDL 138
>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small
GTPase. Rheb (Ras Homolog Enriched in Brain) subfamily.
Rheb was initially identified in rat brain, where its
expression is elevated by seizures or by long-term
potentiation. It is expressed ubiquitously, with
elevated levels in muscle and brain. Rheb functions as
an important mediator between the tuberous sclerosis
complex proteins, TSC1 and TSC2, and the mammalian
target of rapamycin (TOR) kinase to stimulate cell
growth. TOR kinase regulates cell growth by controlling
nutrient availability, growth factors, and the energy
status of the cell. TSC1 and TSC2 form a dimeric complex
that has tumor suppressor activity, and TSC2 is a GTPase
activating protein (GAP) for Rheb. The TSC1/TSC2 complex
inhibits the activation of TOR kinase through Rheb. Rheb
has also been shown to induce the formation of large
cytoplasmic vacuoles in a process that is dependent on
the GTPase cycle of Rheb, but independent of the TOR
kinase, suggesting Rheb plays a role in endocytic
trafficking that leads to cell growth and cell-cycle
progression. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 180
Score = 35.3 bits (82), Expect = 0.089
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYIL--IDTAG 239
K+A++G +VGKS+L + + V +Y T ++ + Y ++Y L +DTAG
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYP--TIENTFSKIITYKGQEYHLEIVDTAG 58
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 35.0 bits (81), Expect = 0.11
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGE 205
+++ ++G VGKS+LI SL+ E
Sbjct: 3 VRIVLIGDEGVGKSSLIMSLVSE 25
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 35.7 bits (83), Expect = 0.18
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 184 KVAIVGKPNVGKSTLINSLLG 204
+VA+VG GKSTL+N LLG
Sbjct: 350 RVALVGPSGAGKSTLLNLLLG 370
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 35.7 bits (83), Expect = 0.19
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 184 KVAIVGKPNVGKSTLINSLLGEN 206
++AIVG GKSTL+ L GE
Sbjct: 350 RIAIVGPNGAGKSTLLKLLAGEL 372
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 35.2 bits (82), Expect = 0.21
Identities = 10/21 (47%), Positives = 17/21 (80%)
Query: 184 KVAIVGKPNVGKSTLINSLLG 204
++A+VG GK++L+N+LLG
Sbjct: 378 RIALVGPSGAGKTSLLNALLG 398
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 34.0 bits (79), Expect = 0.23
Identities = 28/93 (30%), Positives = 40/93 (43%), Gaps = 16/93 (17%)
Query: 84 DIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINK-------SENIN------SSISL 130
DI I +V G++ Q N + + PI++ INK + S + L
Sbjct: 74 DIAILVVAADDGVMPQTIEAINHAKAANVPIIVAINKIDKPYGTEADPERVKNELSELGL 133
Query: 131 DFYELGIGNPHI--ISALYGNGIKNFLENILTI 161
E G G+ I ISA G GI + LE IL +
Sbjct: 134 VGEEWG-GDVSIVPISAKTGEGIDDLLEAILLL 165
>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine
triphosphatases (GTPases). Members of the Rho (Ras
homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1,
RhoBTB, and Rop. There are 22 human Rho family members
identified currently. These proteins are all involved in
the reorganization of the actin cytoskeleton in response
to external stimuli. They also have roles in cell
transformation by Ras in cytokinesis, in focal adhesion
formation and in the stimulation of stress-activated
kinase. These various functions are controlled through
distinct effector proteins and mediated through a
GTP-binding/GTPase cycle involving three classes of
regulating proteins: GAPs (GTPase-activating proteins),
GEFs (guanine nucleotide exchange factors), and GDIs
(guanine nucleotide dissociation inhibitors). Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Since crystal structures
often lack C-terminal residues, this feature is not
available for annotation in many of the CDs in the
hierarchy.
Length = 171
Score = 33.7 bits (78), Expect = 0.29
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 18/66 (27%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFE-------YNNKKYILI 235
IK+ +VG VGK+ L+ I+Y T + + ++F+ + K+ L
Sbjct: 1 IKIVVVGDGAVGKTCLL---------ISYTTNKFPTEYVPTVFDNYSANVTVDGKQVNLG 51
Query: 236 --DTAG 239
DTAG
Sbjct: 52 LWDTAG 57
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 33.6 bits (77), Expect = 0.34
Identities = 35/157 (22%), Positives = 64/157 (40%), Gaps = 38/157 (24%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYN-----NKKYILIDTAG 239
V I G + GK++L L T T T S + Y + LID G
Sbjct: 6 VIIAGLCDSGKTSLFTLL-------TTGTVKKTVTSQEPSAAYKYMLHKGFSFTLIDFPG 58
Query: 240 -IRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDA---QQNISAQDINIANFIYE---- 291
++ R K E I+ S ++ + + ++D+ + ++ + A F+YE
Sbjct: 59 HVKLRQKLLETIKDSSSLRGI---------VFVVDSTAFPKEVT----DTAEFLYEILSI 105
Query: 292 -----SGRSLIVCVNKWDSIIHNQRKIIKNNIKKKLN 323
+G +++ NK +S K IK ++K++N
Sbjct: 106 TELLKNGIDILIACNKQESFTARPPKKIKQALEKEIN 142
Score = 32.8 bits (75), Expect = 0.56
Identities = 29/134 (21%), Positives = 56/134 (41%), Gaps = 26/134 (19%)
Query: 2 KPVLVLVGRPNVGKSTLFNRLTNS--RDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGG 59
+P +++ G + GK++LF LT + + + P +G SF +ID G
Sbjct: 3 QPAVIIAGLCDSGKTSLFTLLTTGTVKKTVTSQEPSAAYKYMLHKG----FSFTLIDFPG 58
Query: 60 FEPEVKKGIMHEMTKQTKQAIIESDI---IIFIVDG---RQGLVEQ-----DKLITNFLR 108
++ ++ + I +S I+F+VD + + + + L L
Sbjct: 59 HV---------KLRQKLLETIKDSSSLRGIVFVVDSTAFPKEVTDTAEFLYEILSITELL 109
Query: 109 KSGQPIVLVINKSE 122
K+G I++ NK E
Sbjct: 110 KNGIDILIACNKQE 123
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 34.1 bits (79), Expect = 0.34
Identities = 32/149 (21%), Positives = 57/149 (38%), Gaps = 32/149 (21%)
Query: 5 LVLVGRPNVGKSTLF----------NRLTNSRDA-LVANYPGLTRDRHYGE-------GY 46
+ LVG GK+TL +RL D V++Y + R +
Sbjct: 2 IALVGHSGSGKTTLAEALLYATGAIDRLGRVEDGNTVSDYDPEEKKRKMSIETSVAPLEW 61
Query: 47 IGKKSFIIIDTGGFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNF 106
G K +I DT G+ + +T A+ D + +V+ + G+ + + F
Sbjct: 62 NGHKINLI-DTPGYA---------DFVGETLSALRAVDAALIVVEAQSGVEVGTEKVWEF 111
Query: 107 LRKSGQPIVLVINKSENINSSISLDFYEL 135
L + P ++ INK + + DF +
Sbjct: 112 LDDAKLPRIIFINKMDRARA----DFDKT 136
Score = 33.3 bits (77), Expect = 0.66
Identities = 31/139 (22%), Positives = 53/139 (38%), Gaps = 32/139 (23%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRD----------------SIKS---LF 225
+A+VG GK+TL +LL I D G D SI++
Sbjct: 2 IALVGHSGSGKTTLAEALLYATGAI--DRLGRVEDGNTVSDYDPEEKKRKMSIETSVAPL 59
Query: 226 EYNNKKYILIDTAGIRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINI 285
E+N K LIDT G + E + + +++++AQ + +
Sbjct: 60 EWNGHKINLIDTPGY--ADFVGETLSALRA---------VDAALIVVEAQSGVEVGTEKV 108
Query: 286 ANFIYESGRSLIVCVNKWD 304
F+ ++ I+ +NK D
Sbjct: 109 WEFLDDAKLPRIIFINKMD 127
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 34.8 bits (80), Expect = 0.35
Identities = 43/172 (25%), Positives = 72/172 (41%), Gaps = 25/172 (14%)
Query: 3 PVLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKS----FIIIDTG 58
P++ ++G + GK+TL +++ ++ A G+T+ E K + +DT
Sbjct: 245 PIVTILGHVDHGKTTLLDKIRKTQIA-QKEAGGITQKIGAYEVEFEYKDENQKIVFLDTP 303
Query: 59 GFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVI 118
G E + + +DI I I+ G+ Q N+++ + PI++ I
Sbjct: 304 GHEA---------FSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVPIIVAI 354
Query: 119 NKSENINSSI-----SLDFYEL-----GIGNPHI-ISALYGNGIKNFLENIL 159
NK + N++ L Y L G P I ISA G I LE IL
Sbjct: 355 NKIDKANANTERIKQQLAKYNLIPEKWGGDTPMIPISASQGTNIDKLLETIL 406
Score = 34.4 bits (79), Expect = 0.40
Identities = 62/279 (22%), Positives = 108/279 (38%), Gaps = 49/279 (17%)
Query: 105 NFLRKSGQPIVLVINKSENINSSISLDFYELG----IGNPHIISALYGNGI--------- 151
L + I NK ++I+ L EL I II +L+ GI
Sbjct: 141 KVLSSKDELIKYDNNKPKSISIHSPLTIQELSTLLCIPETEIIKSLFLKGISVTVNQIID 200
Query: 152 --------KNFLENILTIELPYKKFFK-KKEFTNIHSIEYIK----VAIVGKPNVGKSTL 198
+F NI++ E + T+ + I V I+G + GK+TL
Sbjct: 201 ISIISQVADDFGINIISEEKNNINEKTSNLDNTSAFTENSINRPPIVTILGHVDHGKTTL 260
Query: 199 INSLLGENRVITYDTPGTTRDSIKSL---FEYN--NKKYILIDTAGIRRRNKTFEVIEKF 253
++ + I G I + FEY N+K + +DT G E F
Sbjct: 261 LDKIRKTQ--IAQKEAGGITQKIGAYEVEFEYKDENQKIVFLDTPGH----------EAF 308
Query: 254 SVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCVNKWD----SIIHN 309
S ++ + ++ IL++ A + Q I N+I + +IV +NK D +
Sbjct: 309 SSMR-SRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVPIIVAINKIDKANANTERI 367
Query: 310 QRKIIKNNIKKKLNFLSFAMFNFISAIKLNNINSFMESI 348
++++ K N+ + + ISA + NI+ +E+I
Sbjct: 368 KQQLAKYNLIPE-KWGGDTPMIPISASQGTNIDKLLETI 405
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 33.9 bits (78), Expect = 0.37
Identities = 13/19 (68%), Positives = 15/19 (78%)
Query: 185 VAIVGKPNVGKSTLINSLL 203
V +VG P VGKSTLI SL+
Sbjct: 42 VVVVGPPGVGKSTLIRSLI 60
>gnl|CDD|206651 cd01852, AIG1, AvrRpt2-Induced Gene 1 (AIG1). This group
represents Arabidoposis protein AIG1 (avrRpt2-induced
gene 1) that appears to be involved in plant resistance
to bacteria. The Arabidopsis disease resistance gene
RPS2 is involved in recognition of bacterial pathogens
carrying the avirulence gene avrRpt2. AIG1 exhibits
RPS2- and avrRpt1-dependent induction early after
infection with Pseudomonas syringae carrying avrRpt2.
This subfamily also includes IAN-4 protein, which has
GTP-binding activity and shares sequence homology with a
novel family of putative GTP-binding proteins: the
immuno-associated nucleotide (IAN) family. The
evolutionary conservation of the IAN family provides a
unique example of a plant pathogen response gene
conserved in animals. The IAN/IMAP subfamily has been
proposed to regulate apoptosis in vertebrates and
angiosperm plants, particularly in relation to cancer,
diabetes, and infections. The human IAN genes were
renamed GIMAP (GTPase of the immunity associated
proteins).
Length = 201
Score = 33.7 bits (78), Expect = 0.37
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRVIT-YDTPGTTRDSIKSLFEYNNKKYILIDTAGI 240
+++ +VGK GKS N++LG + G T+ K ++ ++ +IDT G+
Sbjct: 1 LRLVLVGKTGNGKSATGNTILGRKVFESKLSASGVTKTCQKESAVWDGRRVNVIDTPGL 59
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is equally
distributed between a soluble cytoplasmic form and a
membrane-inserted form, suggesting that assembly of the
Toc complex is dynamic. Toc34 and Toc75 act sequentially
to mediate docking and insertion of Toc159 resulting in
assembly of the functional translocon.
Length = 248
Score = 33.4 bits (77), Expect = 0.51
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 12/63 (19%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVIT--YDTPGTTR----DSIKSLFEYNNKKYILIDTA 238
+ ++GK VGKS+ INS+ GE +V + T R F+ N +IDT
Sbjct: 34 ILVLGKTGVGKSSTINSIFGERKVSVSAFQ-SETLRPREVSRTVDGFKLN-----IIDTP 87
Query: 239 GIR 241
G+
Sbjct: 88 GLL 90
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 33.7 bits (78), Expect = 0.60
Identities = 14/30 (46%), Positives = 22/30 (73%), Gaps = 1/30 (3%)
Query: 184 KVAI-VGKPNVGKSTLINSLLGENRVITYD 212
+++I VG+ VGKS+LIN+LL E ++ D
Sbjct: 206 RISIFVGQSGVGKSSLINALLPEAEILVGD 235
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 34.1 bits (79), Expect = 0.60
Identities = 33/124 (26%), Positives = 53/124 (42%), Gaps = 38/124 (30%)
Query: 49 KKSFIIIDTGGFEPEVKKGIMHE-----MTKQTKQAIIESDIIIFIVDGRQGLVEQDK-- 101
K+ FI+ DT G HE M A D+ I +VD R+G++ Q +
Sbjct: 103 KRKFIVADTPG----------HEQYTRNMVTGASTA----DLAIILVDARKGVLTQTRRH 148
Query: 102 -LITNFLRKSG-QPIVLVINK------SENINSSISLDFY----ELGIGNPHII--SALY 147
I + L G + +VL +NK + + I D+ +LG+ + I SAL
Sbjct: 149 SFIASLL---GIRHVVLAVNKMDLVDYDQEVFDEIVADYRAFAAKLGLHDVTFIPISALK 205
Query: 148 GNGI 151
G+ +
Sbjct: 206 GDNV 209
>gnl|CDD|183094 PRK11347, PRK11347, antitoxin ChpS; Provisional.
Length = 83
Score = 30.8 bits (69), Expect = 0.70
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 737 AVSLHASNNNLRNKLVPISKKYPLKELILAC 767
+V SNN L L PIS++Y L EL+ C
Sbjct: 31 SVEAQVSNNQL--ILTPISRRYSLDELLAQC 59
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA ternary
complex to the ribosomal A site by facilitated release
of the deacylated tRNA from the E site. The reaction
requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 32.0 bits (74), Expect = 0.71
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 184 KVAIVGKPNVGKSTLINSLLGE 205
++ +VG+ GKSTL+ + GE
Sbjct: 28 RIGLVGRNGAGKSTLLKLIAGE 49
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 32.2 bits (74), Expect = 0.86
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRV----ITYDTPGTTRDSIKSL 224
VA+VG GKSTL+ ++ G + I D + ++ L
Sbjct: 28 VALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEEL 71
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 32.6 bits (75), Expect = 0.87
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 181 EYIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRD 219
+ IKV I G P +GK++L +L + + D GTT+
Sbjct: 2 KNIKVLIYGPPGIGKTSLAKTLPPKTLFLDLD-AGTTKV 39
>gnl|CDD|129200 TIGR00092, TIGR00092, GTP-binding protein YchF. This predicted
GTP-binding protein is found in a single copy in every
complete bacterial genome, and is found in Eukaryotes.
A more distantly related protein, separated from this
model, is found in the archaea. It is known to bind GTP
and double-stranded nucleic acid. It is suggested to
belong to a nucleoprotein complex and act as a
translation factor [Unknown function, General].
Length = 368
Score = 33.2 bits (76), Expect = 0.88
Identities = 17/31 (54%), Positives = 18/31 (58%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLT 37
+VG PNVGKSTLF TN AN P T
Sbjct: 7 IVGLPNVGKSTLFAATTNLLGNEAANPPFTT 37
>gnl|CDD|133345 cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3. The
M-Ras/R-Ras-like subfamily contains R-Ras2/TC21,
M-Ras/R-Ras3, and related members of the Ras family.
M-Ras is expressed in lympho-hematopoetic cells. It
interacts with some of the known Ras effectors, but
appears to also have its own effectors. Expression of
mutated M-Ras leads to transformation of several types
of cell lines, including hematopoietic cells, mammary
epithelial cells, and fibroblasts. Overexpression of
M-Ras is observed in carcinomas from breast, uterus,
thyroid, stomach, colon, kidney, lung, and rectum. In
addition, expression of a constitutively active M-Ras
mutant in murine bone marrow induces a malignant mast
cell leukemia that is distinct from the monocytic
leukemia induced by H-Ras. TC21, along with H-Ras, has
been shown to regulate the branching morphogenesis of
ureteric bud cell branching in mice. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 32.0 bits (73), Expect = 0.93
Identities = 36/126 (28%), Positives = 55/126 (43%), Gaps = 14/126 (11%)
Query: 5 LVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFI--IIDTGGFEP 62
LV+VG VGKS L + S V +Y D + + I + I+DT G E
Sbjct: 5 LVVVGGGGVGKSALTIQFIQSY--FVTDYDPTIEDSYTKQCEIDGQWARLDILDTAGQE- 61
Query: 63 EVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLR---KSGQPIVLVIN 119
+ M E +T + +++F V R E DK T LR + P++LV N
Sbjct: 62 --EFSAMREQYMRTGEGF----LLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGN 115
Query: 120 KSENIN 125
K++ +
Sbjct: 116 KADLEH 121
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 32.2 bits (74), Expect = 0.96
Identities = 10/22 (45%), Positives = 18/22 (81%)
Query: 185 VAIVGKPNVGKSTLINSLLGEN 206
+A+VG + GKS+++N+LLG +
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRD 22
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however, Miro
is one of few Rho subfamilies that lack this feature.
Length = 180
Score = 32.2 bits (74), Expect = 1.00
Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 13/89 (14%)
Query: 187 IVGKPNVGKSTLINSLLGENRVITYDTPGT-TRDSIKSLFEYNNKKYILIDTAGIRRRNK 245
++G GKS L+ + LG + +P R ++ ++ +KY+++
Sbjct: 9 VLGAKGSGKSALLQAFLGRSFSQNAYSPTIKPRYAVNTVEVPGQEKYLIL---------- 58
Query: 246 TFEVIEKFSVIKTLKSILEA-NVVILLLD 273
EV E I + L A +V L+ D
Sbjct: 59 -REVGEDEEAILLNDAELAACDVACLVYD 86
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 33.1 bits (76), Expect = 1.1
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 184 KVAIVGKPNVGKSTLINSLLG 204
KVAI+G+ GKSTL+ L G
Sbjct: 366 KVAILGRSGSGKSTLLQLLAG 386
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 31.6 bits (71), Expect = 1.1
Identities = 25/137 (18%), Positives = 41/137 (29%), Gaps = 23/137 (16%)
Query: 184 KVAIVGKPNVGKSTLINSLLGE----NRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAG 239
+ IVG P GK+TL +L E + Y + + +G
Sbjct: 4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSG 63
Query: 240 IRRRNKTFEVIEKFSVIKTLKSILEANVVIL-----LLDAQQNISAQDIN----IANFIY 290
R + K V+IL LLDA+Q + +
Sbjct: 64 ELRLRLALALARKLKPD----------VLILDEITSLLDAEQEALLLLLEELRLLLLLKS 113
Query: 291 ESGRSLIVCVNKWDSII 307
E ++I+ N +
Sbjct: 114 EKNLTVILTTNDEKDLG 130
>gnl|CDD|215753 pfam00152, tRNA-synt_2, tRNA synthetases class II (D, K and N).
Length = 345
Score = 32.6 bits (75), Expect = 1.2
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 1100 RYDFLIKKFSNKFVPASGFAIGIERLIELI 1129
++ F + P G +G++RL+ L+
Sbjct: 299 KFGFYLDALKYGMPPHGGIGLGLDRLVMLL 328
>gnl|CDD|110998 pfam02055, Glyco_hydro_30, O-Glycosyl hydrolase family 30.
Length = 495
Score = 33.0 bits (75), Expect = 1.3
Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 8/70 (11%)
Query: 889 NLSLRPEGTASVIRSVIENNLIYDGPKRLWYSGPMFRHERPQYGRYRQFYQIGVEAIGF- 947
NL+L EG S + + ++ +I K +Y PMF + F + G I
Sbjct: 378 NLALDAEGGPSWVSNFVDAPVIAFPAKAQFYKQPMFYA----IAHFSHFIKPGAVRIDHS 433
Query: 948 ---PGPDIDA 954
P+++A
Sbjct: 434 LNQKNPELEA 443
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They belong
to the subfamily C of the ATP-binding cassette (ABC)
superfamily of transport proteins. The ABCC subfamily
contains transporters with a diverse functional spectrum
that includes ion transport, cell surface receptor, and
toxin secretion activities. The MRP-like family, similar
to all ABC proteins, have a common four-domain core
structure constituted by two membrane-spanning domains,
each composed of six transmembrane (TM) helices, and two
nucleotide-binding domains (NBD). ABC transporters are a
subset of nucleotide hydrolases that contain a signature
motif, Q-loop, and H-loop/switch region, in addition to,
the Walker A motif/P-loop and Walker B motif commonly
found in a number of ATP- and GTP-binding and
hydrolyzing proteins.
Length = 171
Score = 31.6 bits (73), Expect = 1.3
Identities = 13/21 (61%), Positives = 14/21 (66%)
Query: 184 KVAIVGKPNVGKSTLINSLLG 204
KVAIVG GKSTL+ LL
Sbjct: 30 KVAIVGPSGSGKSTLLKLLLR 50
>gnl|CDD|227321 COG4988, CydD, ABC-type transport system involved in cytochrome bd
biosynthesis, ATPase and permease components [Energy
production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 559
Score = 32.6 bits (75), Expect = 1.4
Identities = 13/41 (31%), Positives = 16/41 (39%), Gaps = 2/41 (4%)
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVIT--YDTPGTTRDSIK 222
A+VG GKSTL+N LLG G +
Sbjct: 349 LTALVGASGAGKSTLLNLLLGFLAPTQGEIRVNGIDLRDLS 389
>gnl|CDD|233224 TIGR00993, 3a0901s04IAP86, chloroplast protein import component
Toc86/159, G and M domains. The long precursor of the
86K protein originally described is proposed to have
three domains. The N-terminal A-domain is acidic,
repetitive, weakly conserved, readily removed by
proteolysis during chloroplast isolation, and not
required for protein translocation. The other domains
are designated G (GTPase) and M (membrane anchor); this
family includes most of the G domain and all of M
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 763
Score = 33.0 bits (75), Expect = 1.4
Identities = 27/104 (25%), Positives = 52/104 (50%), Gaps = 9/104 (8%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRV-ITYDTPGTTR-DSIKSLFEYNNKKYILIDTAGIRR 242
+ ++GK VGKS INS+ GE + GTT I+ L K +IDT G+
Sbjct: 121 ILVLGKSGVGKSATINSIFGEVKFSTDAFGMGTTSVQEIEGLV--QGVKIRVIDTPGL-- 176
Query: 243 RNKTFEVIEKFSVIKTLKSILEANV--VILLLDAQQNISAQDIN 284
++ + + ++ ++K ++ N ++L +D + ++ +D N
Sbjct: 177 KSSASDQSKNEKILSSVKKFIKKNPPDIVLYVD-RLDMQTRDSN 219
>gnl|CDD|213221 cd03254, ABCC_Glucan_exporter_like, ATP-binding cassette domain of
glucan transporter and related proteins, subfamily C.
Glucan exporter ATP-binding protein. In A. tumefaciens
cyclic beta-1, 2-glucan must be transported into the
periplasmic space to exert its action as a virulence
factor. This subfamily belongs to the MRP-like family
and is involved in drug, peptide, and lipid export. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains each composed of six
transmembrane (TM) helices and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 229
Score = 32.2 bits (74), Expect = 1.5
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 184 KVAIVGKPNVGKSTLINSLLG 204
VAIVG GK+TLIN L+
Sbjct: 31 TVAIVGPTGAGKTTLINLLMR 51
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 31.3 bits (72), Expect = 1.6
Identities = 42/181 (23%), Positives = 70/181 (38%), Gaps = 39/181 (21%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKS-LFEYNNKKYILI--DTAG 239
K+ ++G VGK++L+ + Y + T KS E + KK L DTAG
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKS--TIGVDFKSKTIEVDGKKVKLQIWDTAG 58
Query: 240 IRRRNKTFEVIEKFSVIKTLKSILE-----ANVVILLLDAQQNISAQDI-NIANFIYESG 293
E+F +SI A+ IL+ D S +++ N + E
Sbjct: 59 ----------QERF------RSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYA 102
Query: 294 RSLIVCV---NKWDSIIHNQRKIIKNNIK---KKLNFLSFAMFNFISAIKLNNINSFMES 347
I + NK D + ++R++ + K+ L F SA N++ ES
Sbjct: 103 PPNIPIILVGNKSD--LEDERQVSTEEAQQFAKENGLLFF----ETSAKTGENVDEAFES 156
Query: 348 I 348
+
Sbjct: 157 L 157
>gnl|CDD|226647 COG4181, COG4181, Predicted ABC-type transport system involved in
lysophospholipase L1 biosynthesis, ATPase component
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 228
Score = 32.0 bits (73), Expect = 1.7
Identities = 27/89 (30%), Positives = 39/89 (43%), Gaps = 11/89 (12%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRRRN 244
VAIVG GKSTL+ L G + + G R + L + + A +R R+
Sbjct: 39 VAIVGPSGSGKSTLLAVLAGLDDP----SSGEVRLLGQPLHKLDEDA-----RAALRARH 89
Query: 245 KTFEVIEKFSVIKTLKSILEANVVILLLD 273
F V + F +I L + LE + L L
Sbjct: 90 VGF-VFQSFHLIPNL-TALENVALPLELR 116
>gnl|CDD|236515 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
Length = 332
Score = 32.1 bits (74), Expect = 1.7
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 183 IKVAIVGKPNVGKSTLINSL 202
+++ I G P VGKST I +L
Sbjct: 57 LRIGITGVPGVGKSTFIEAL 76
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 31.4 bits (72), Expect = 1.8
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 184 KVAIVGKPNVGKSTLINSL 202
++ I G P+ GK+TL+ +L
Sbjct: 1 RIVITGGPSTGKTTLLEAL 19
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 31.8 bits (73), Expect = 1.8
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 5/45 (11%)
Query: 185 VAIVGKPNVGKSTLINSLLG-----ENRVITYDTPGTTRDSIKSL 224
V ++G GKSTL+ L G V+ ++ S+ L
Sbjct: 33 VLLIGPNGSGKSTLLKLLNGLLKPTSGEVLVDGLDTSSEKSLLEL 77
>gnl|CDD|217547 pfam03419, Peptidase_U4, Sporulation factor SpoIIGA.
Length = 291
Score = 31.8 bits (73), Expect = 1.8
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 6/62 (9%)
Query: 1105 IKKFSNKFVPASGFAIG---IERLIELIKKININHNFSHQCDIYIVHVGKEAELKAFVLS 1161
S KFV GF I +R E IK+ I + ++ IV GK+ +K V +
Sbjct: 121 GDPISWKFVLI-GFPILYIFSKRRWEYIKRRKIQYEL--IVEVEIVINGKKLNVKGLVDT 177
Query: 1162 EN 1163
N
Sbjct: 178 GN 179
>gnl|CDD|214541 smart00173, RAS, Ras subfamily of RAS small GTPases. Similar in
fold and function to the bacterial EF-Tu GTPase. p21Ras
couples receptor Tyr kinases and G protein receptors to
protein kinase cascades.
Length = 164
Score = 31.0 bits (71), Expect = 1.9
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYIL--IDTAG 239
K+ ++G VGKS L + + V YD P T DS + E + + +L +DTAG
Sbjct: 2 KLVVLGSGGVGKSALTIQFIQGHFVDDYD-P-TIEDSYRKQIEIDGEVCLLDILDTAG 57
>gnl|CDD|133377 cd04177, RSR1, RSR1/Bud1p family GTPase. RSR1/Bud1p is a member of
the Rap subfamily of the Ras family that is found in
fungi. In budding yeasts, RSR1 is involved in selecting
a site for bud growth on the cell cortex, which directs
the establishment of cell polarization. The Rho family
GTPase cdc42 and its GEF, cdc24, then establish an axis
of polarized growth by organizing the actin cytoskeleton
and secretory apparatus at the bud site. It is believed
that cdc42 interacts directly with RSR1 in vivo. In
filamentous fungi, polar growth occurs at the tips of
hypha and at novel growth sites along the extending
hypha. In Ashbya gossypii, RSR1 is a key regulator of
hyphal growth, localizing at the tip region and
regulating in apical polarization of the actin
cytoskeleton. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 168
Score = 31.3 bits (71), Expect = 1.9
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYIL--IDTAGI 240
K+ ++G VGKS L + + +YD T DS + E + ++ L +DTAG
Sbjct: 3 KIVVLGAGGVGKSALTVQFVQNVFIESYDP--TIEDSYRKQVEIDGRQCDLEILDTAGT 59
>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily;
ill-defined subfamily. SMART predicts Ras-like small
GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies.
Others that could not be classified in this way are
predicted to be members of the small GTPase superfamily
without predictions of the subfamily.
Length = 166
Score = 31.0 bits (71), Expect = 2.0
Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 5/61 (8%)
Query: 181 EYIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYIL--IDTA 238
EY K+ ++G VGKS L + + V YD P T DS + E + + +L +DTA
Sbjct: 2 EY-KLVVLGGGGVGKSALTIQFVQGHFVDEYD-P-TIEDSYRKQIEIDGEVCLLDILDTA 58
Query: 239 G 239
G
Sbjct: 59 G 59
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 32.2 bits (74), Expect = 2.0
Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 11/68 (16%)
Query: 54 IIDTGGFEPEVKKGIMH-EMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQ 112
+IDT G H + T + ++++ D + +VD +G+ Q + + K G
Sbjct: 80 LIDTPG----------HVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTETVWRQADKYGV 129
Query: 113 PIVLVINK 120
P +L +NK
Sbjct: 130 PRILFVNK 137
>gnl|CDD|206708 cd04136, Rap_like, Rap-like family consists of Rap1, Rap2 and RSR1.
The Rap subfamily consists of the Rap1, Rap2, and RSR1.
Rap subfamily proteins perform different cellular
functions, depending on the isoform and its subcellular
localization. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and microsomal
membrane of the pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. Rap1 localizes in the nucleus of human
oropharyngeal squamous cell carcinomas (SCCs) and cell
lines. Rap1 plays a role in phagocytosis by controlling
the binding of adhesion receptors (typically integrins)
to their ligands. In yeast, Rap1 has been implicated in
multiple functions, including activation and silencing
of transcription and maintenance of telomeres. Rap2 is
involved in multiple functions, including activation of
c-Jun N-terminal kinase (JNK) to regulate the actin
cytoskeleton and activation of the Wnt/beta-catenin
signaling pathway in embryonic Xenopus. A number of
effector proteins for Rap2 have been identified,
including isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK), and the
RalGEFs RalGDS, RGL, and Rlf, which also interact with
Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and
Rap2. In budding yeasts, it is involved in selecting a
site for bud growth, which directs the establishment of
cell polarization. The Rho family GTPase Cdc42 and its
GEF, Cdc24, then establish an axis of polarized growth.
It is believed that Cdc42 interacts directly with RSR1
in vivo. In filamentous fungi such as Ashbya gossypii,
RSR1 is a key regulator of polar growth in the hypha.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 164
Score = 31.0 bits (70), Expect = 2.0
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 181 EYIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYIL--IDTA 238
EY K+ ++G VGKS L + V YD T DS + E + ++ +L +DTA
Sbjct: 1 EY-KLVVLGSGGVGKSALTVQFVQGIFVDKYDP--TIEDSYRKQIEVDCQQCMLEILDTA 57
Query: 239 GI 240
G
Sbjct: 58 GT 59
>gnl|CDD|237894 PRK15064, PRK15064, ABC transporter ATP-binding protein;
Provisional.
Length = 530
Score = 32.2 bits (74), Expect = 2.0
Identities = 11/22 (50%), Positives = 19/22 (86%)
Query: 184 KVAIVGKPNVGKSTLINSLLGE 205
++AI+G+ VGK+TL+ +L+GE
Sbjct: 347 RLAIIGENGVGKTTLLRTLVGE 368
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 31.0 bits (71), Expect = 2.1
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAG 239
++ ++G GK+T++ L V T T G +++++ EY N K+ + D G
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVVTTIPTIGF---NVETV-EYKNVKFTVWDVGG 52
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 30.3 bits (69), Expect = 2.1
Identities = 19/124 (15%), Positives = 37/124 (29%), Gaps = 25/124 (20%)
Query: 185 VAIVGKPNVGKSTLINSL---LGENRVITYDTPGTT-----RDSIKSLFEYNNKKYILID 236
+ G+ GK+TL+ L L RV+ + P I
Sbjct: 7 GVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSG----- 61
Query: 237 TAGIRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSL 296
+ E I + +L++D Q++S + + +Y+
Sbjct: 62 ----GTTAELLEAILDA--------LKRRGRPLLIIDEAQHLSLEALEELRDLYDLSEKG 109
Query: 297 IVCV 300
I +
Sbjct: 110 IQVI 113
Score = 28.8 bits (65), Expect = 7.1
Identities = 24/123 (19%), Positives = 40/123 (32%), Gaps = 18/123 (14%)
Query: 2 KPVLVLVGRPNVGKSTLFNRLTNS---RDALVANYPGLTRDRHYGEGYIGKKSFIIIDTG 58
+ VL G GK+TL RL R + P L K +
Sbjct: 4 AGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLG----------TPKDLLRKILR 53
Query: 59 GFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQD----KLITNFLRKSGQPI 114
+ G E+ + A+ + I+D Q L + + + + K Q +
Sbjct: 54 ALGLPLSGGTTAELLEAILDALKRRGRPLLIIDEAQHLSLEALEELRDLYDLSEKGIQ-V 112
Query: 115 VLV 117
+LV
Sbjct: 113 ILV 115
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 32.4 bits (73), Expect = 2.2
Identities = 31/116 (26%), Positives = 45/116 (38%), Gaps = 18/116 (15%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAGIRRRN 244
VA+VG P GKSTLI SL+ R T T R I +G RR
Sbjct: 72 VAVVGPPGTGKSTLIRSLV---RRFTKQTIDEIRGPITV-------------VSGKTRRI 115
Query: 245 KTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFIYESGRSLIVCV 300
E + + I A++V+LL+D + + N + G ++ V
Sbjct: 116 TFLECPSDLHQMIDVAKI--ADLVLLLIDGNFGFEMETMEFLNILISHGMPRVLGV 169
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 30.4 bits (69), Expect = 2.2
Identities = 22/128 (17%), Positives = 43/128 (33%), Gaps = 33/128 (25%)
Query: 185 VAIVGKPNVGKSTLINSLLGE-----NRVITY----------DTPGTTRDSIKSLFEYNN 229
V +VG + GK+TLI LL RV D PG + +
Sbjct: 3 VLVVGPKDSGKTTLIRKLLNYLKRRGYRVAVVKHLDHGQGEIDKPGKI-----AAL--SI 55
Query: 230 KKYILIDTAGIRRRNKTFE-VIEKFSVI------KTLKSILEANVVILL----LDAQQNI 278
++ + E ++ + S + K+ + +VI+ ++ Q+N
Sbjct: 56 EEPADGPEGFHQEEEMPLEELLSRLSYLVLFEGFKSPSENPKLYIVIVKELAEIEDQRNK 115
Query: 279 SAQDINIA 286
+ +
Sbjct: 116 EEDESGLI 123
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 31.4 bits (72), Expect = 2.2
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 212 DTPGTTRDSIKSLFEYNNKKYILIDTAGIRRRNKTFEVIEKFSVIKTLKSILEANVVILL 271
D D+++ + N +L+DTAG R +N +K +K ++ + V+L+
Sbjct: 67 DPAAVAFDAVEK-AKAENYDVVLVDTAG-RLQNDK----NLMDELKKIKRVIAPDEVLLV 120
Query: 272 LDA--QQNISAQ 281
LDA QN Q
Sbjct: 121 LDATTGQNALNQ 132
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 30.3 bits (69), Expect = 2.4
Identities = 25/97 (25%), Positives = 41/97 (42%), Gaps = 10/97 (10%)
Query: 185 VAIVGKPNVGKSTLINSLLG--ENRVITY--DTPGTTRDSIKSLFEYNNKKYILIDTAGI 240
V +VG P GKS L L NR + Y T TT + +K + +D +
Sbjct: 2 VLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPLV 61
Query: 241 RR-RNKTFEVIEKF-----SVIKTLKSILEANVVILL 271
R R V+++ V+ +L S+L+ ++L
Sbjct: 62 RAAREGEIAVLDEINRANPDVLNSLLSLLDERRLLLP 98
>gnl|CDD|234357 TIGR03797, NHLM_micro_ABC2, NHLM bacteriocin system ABC
transporter, ATP-binding protein. Members of this
protein family are ABC transporter ATP-binding subunits,
part of a three-gene putative bacteriocin transport
operon. The other subunits include another ATP-binding
subunit (TIGR03796), which has an N-terminal leader
sequence cleavage domain, and an HlyD homolog
(TIGR03794). In a number of genomes, members of protein
families related to nitrile hydratase alpha subunit or
to nif11 have undergone paralogous family expansions,
with members possessing a putative bacteriocin cleavage
region ending with a classic Gly-Gly motif. Those sets
of putative bacteriocins, members of this protein family
and its partners TIGR03794 and TIGR03796, and
cyclodehydratase/docking scaffold fusion proteins of
thiazole/oxazole biosynthesis frequently show correlated
species distribution and co-clustering within many of
those genomes [Transport and binding proteins, Amino
acids, peptides and amines, Cellular processes,
Biosynthesis of natural products].
Length = 686
Score = 31.9 bits (73), Expect = 2.9
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 6/32 (18%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGT 216
VAIVG GKSTL+ LLG ++TP +
Sbjct: 482 VAIVGPSGSGKSTLLRLLLG------FETPES 507
>gnl|CDD|183498 PRK12395, PRK12395, maltoporin; Provisional.
Length = 419
Score = 31.5 bits (71), Expect = 2.9
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 1077 YNRTVFEWTTDKLGSQNSIC-GGGRYDFLIKKFSNKFVPASGFAIGIERLIELIKKININ 1135
YN+ V ++ L +QN I GGG YD +K A G+ + LI + K + N
Sbjct: 250 YNKLVLQYANKGL-AQNMISQGGGWYDMW-----HKTDEAKGYRVINTGLIPITDKFSFN 303
Query: 1136 HNFS 1139
H +
Sbjct: 304 HVLT 307
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 31.7 bits (72), Expect = 3.0
Identities = 38/144 (26%), Positives = 57/144 (39%), Gaps = 34/144 (23%)
Query: 3 PVLVLVGRPNVGKSTLFNRLTNSRDALVANYPG-LTRDRHYGEGYIG-----------KK 50
P++ ++G + GK+TL +++ S A+ G +T+ H G I K
Sbjct: 5 PIVSVLGHVDHGKTTLLDKIRGS--AVAKREAGGITQ--HIGATEIPMDVIEGICGDLLK 60
Query: 51 SFII---------IDTGGFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDK 101
F I IDT G E T K+ +D+ I IVD +G Q +
Sbjct: 61 KFKIRLKIPGLLFIDTPGHEA---------FTNLRKRGGALADLAILIVDINEGFKPQTQ 111
Query: 102 LITNFLRKSGQPIVLVINKSENIN 125
N LR P V+ NK + I
Sbjct: 112 EALNILRMYKTPFVVAANKIDRIP 135
>gnl|CDD|214583 smart00247, XTALbg, Beta/gamma crystallins. Beta/gamma
crystallins.
Length = 82
Score = 29.0 bits (66), Expect = 3.2
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 884 ELNGDNLSLRPEGTASVIRSV-IENN--LIYDGPKRLWYSGPMFRHERPQYGRYRQF 937
EL+ D SL+ G+ + SV +E+ ++Y+ P Y G + E +Y Y+++
Sbjct: 16 ELSDDCPSLQDYGSRDNVSSVRVESGCWVLYEQPN---YRGRQYVLEPGEYPDYQEW 69
>gnl|CDD|213191 cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of
branched-chain amino acid transporter. LivF (TM1139) is
part of the LIV-I bacterial ABC-type two-component
transport system that imports neutral, branched-chain
amino acids. The E. coli branched-chain amino acid
transporter comprises a heterodimer of ABC transporters
(LivF and LivG), a heterodimer of six-helix TM domains
(LivM and LivH), and one of two alternative soluble
periplasmic substrate binding proteins (LivK or LivJ).
ABC transporters are a large family of proteins involved
in the transport of a wide variety of different
compounds, like sugars, ions, peptides, and more complex
organic molecules.
Length = 222
Score = 30.9 bits (71), Expect = 3.4
Identities = 8/20 (40%), Positives = 16/20 (80%)
Query: 185 VAIVGKPNVGKSTLINSLLG 204
VA++G+ GK+TL+ +++G
Sbjct: 29 VALLGRNGAGKTTLLKTIMG 48
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 30.9 bits (71), Expect = 3.5
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 10/62 (16%)
Query: 187 IVGKPNVGKSTLINSLLGENRVITYDTPG-------TTRDSIKSLFEYNNKKYILIDTAG 239
+ G+ VGKSTL+N+L + + T + TT L++ + IDT G
Sbjct: 169 LAGQSGVGKSTLLNALAPDLELKTGEISEALGRGKHTTTHV--ELYDLPGGGLL-IDTPG 225
Query: 240 IR 241
Sbjct: 226 FS 227
>gnl|CDD|107376 cd06381, PBP1_iGluR_delta_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of an orphan family of delta receptors,
GluRdelta1 and GluRdelta2. This CD represents the
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of an orphan family of delta
receptors, GluRdelta1 and GluRdelta2. While this
N-terminal domain belongs to the periplasmic-binding
fold type I superfamily, the glutamate-binding domain of
the iGluR is structurally homologous to the
periplasmic-binding fold type II. The LIVBP-like domain
of iGluRs is thought to play a role in the initial
assembly of iGluR subunits, but it is not well
understood how this domain is arranged and functions in
intact iGluR. Although the delta receptors are a member
of the ionotropic glutamate receptor family, they cannot
be activated by AMPA, kainate, NMDA, glutamate, or any
other ligands. Phylogenetic analysis shows that both
GluRdelta1 and GluRalpha2 are more homologous to
non-NMDA receptors. GluRdelta2 was shown to function as
an AMPA-like receptor by mutation analysis. Moreover,
targeted disruption of GluRdelta2 gene caused motor
coordination impairment, Purkinje cell maturation, and
long-term depression of synaptic transmission. It has
been suggested that GluRdelta2 is the receptor for
cerebellin 1, a glycoprotein of the Clq, and the tumor
necrosis factor family which is secreted from cerebellar
granule cells. Furthermore, recent studies have shown
that the orphan GluRdelta1 plays an essential role in
high-frequency hearing and ionic homeostasis in the
basal cochlea and that the locus encoding GluRdelta1 may
be involved in congenial or acquired high-frequency
hearing loss in humans.
Length = 363
Score = 31.3 bits (71), Expect = 3.5
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 4/65 (6%)
Query: 845 SGIFVTIRKIRGNDINAACGQLSGEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSV 904
GI V ++K+ N A + + E+ + D L L L P G + I +
Sbjct: 164 QGIDVLLQKVDLNISKMATALFTTMRCE----ELNRYRDTLRRALLLLSPNGAYTFIDAS 219
Query: 905 IENNL 909
+E NL
Sbjct: 220 VETNL 224
>gnl|CDD|213211 cd03244, ABCC_MRP_domain2, ATP-binding cassette domain 2 of
multidrug resistance-associated protein. The ABC
subfamily C is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resistance lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 221
Score = 30.5 bits (70), Expect = 4.0
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 176 NIHSIEYIKVAIVGKPNVGKSTLINSLL 203
+I E KV IVG+ GKS+L+ +L
Sbjct: 26 SIKPGE--KVGIVGRTGSGKSSLLLALF 51
>gnl|CDD|201353 pfam00625, Guanylate_kin, Guanylate kinase.
Length = 183
Score = 30.4 bits (69), Expect = 4.0
Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 3/54 (5%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVI-TYDTPGTTRDSIKSLFEYNNKKYILIDT 237
+ + G VGKS + +LL E Y TTR E + K Y +
Sbjct: 5 IVLSGPSGVGKSHIKKALLDEYPEKFGYSVSHTTRP--PRPGEVDGKDYHFVSK 56
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and host
eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 30.3 bits (69), Expect = 4.1
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 13/60 (21%)
Query: 168 FFKKKEFTNIHSIEYIKVAIVGKPNV--------GKSTLINSLLGE----NRVITY-DTP 214
+ + Y+ +A+ + N+ GK+TL+N+LL R+IT DT
Sbjct: 3 DLIAQGTFSPLQAAYLWLAVEARKNILISGGTGSGKTTLLNALLAFIPPDERIITIEDTA 62
>gnl|CDD|184902 PRK14938, PRK14938, Ser-tRNA(Thr) hydrolase; Provisional.
Length = 387
Score = 31.0 bits (70), Expect = 4.4
Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 1146 IVHVGKEAELKAFVLSENLRTLGLKVILNCVFNNIHESFKSQMKRANASNANFAAIIGEN 1205
I+ V K+ + ++E LR G++V ++ ++ +S ++++RA F IIGE
Sbjct: 279 ILPVKKDFLDFSIQVAERLRKEGIRVNVD----DLDDSLGNKIRRAGTEWIPFVIIIGER 334
Query: 1206 EIINNTLIIKDLRNKYE 1222
E+ +TL +K +R E
Sbjct: 335 EVKTSTLTVK-IRANNE 350
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 30.8 bits (70), Expect = 4.5
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 222 KSLFEYNNKKYILIDTAG 239
++L +K ILIDTAG
Sbjct: 266 EALDRLRDKDLILIDTAG 283
>gnl|CDD|213202 cd03235, ABC_Metallic_Cations, ATP-binding cassette domain of the
metal-type transporters. This family includes
transporters involved in the uptake of various metallic
cations such as iron, manganese, and zinc. The ATPases
of this group of transporters are very similar to
members of iron-siderophore uptake family suggesting
that they share a common ancestor. The best
characterized metal-type ABC transporters are the
YfeABCD system of Y. pestis, the SitABCD system of
Salmonella enterica serovar Typhimurium, and the SitABCD
transporter of Shigella flexneri. Moreover other
uncharacterized homologs of these metal-type
transporters are mainly found in pathogens like
Haemophilus or enteroinvasive E. coli isolates.
Length = 213
Score = 30.2 bits (69), Expect = 5.0
Identities = 13/21 (61%), Positives = 17/21 (80%), Gaps = 2/21 (9%)
Query: 185 VAIVGKPN-VGKSTLINSLLG 204
+AIVG PN GKSTL+ ++LG
Sbjct: 28 LAIVG-PNGAGKSTLLKAILG 47
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 30.2 bits (69), Expect = 5.1
Identities = 21/95 (22%), Positives = 41/95 (43%), Gaps = 16/95 (16%)
Query: 187 IVGKPNVGKSTL-----INSLLGENRVITYDTPGTTRDSIKSLFEYNNK---KYILIDTA 238
I G P GK+ + + + +VI DT G + + K + + + I+I
Sbjct: 28 IYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTEGLSPERFKQIAGEDFEELLSNIIIFEP 87
Query: 239 GIRRRNKTFEVIEKFSVIKTLKSILEANVVILLLD 273
+FE E+ I+ + + + NV +++LD
Sbjct: 88 ------SSFE--EQSEAIRKAEKLAKENVGLIVLD 114
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component of
iron-siderophores, vitamin B12 and hemin transporters
and related proteins. ABC transporters, involved in the
uptake of siderophores, heme, and vitamin B12, are
widely conserved in bacteria and archaea. Only very few
species lack representatives of the siderophore family
transporters. The E. coli BtuCD protein is an ABC
transporter mediating vitamin B12 uptake. The two
ATP-binding cassettes (BtuD) are in close contact with
each other, as are the two membrane-spanning subunits
(BtuC); this arrangement is distinct from that observed
for the E. coli lipid flippase MsbA. The BtuC subunits
provide 20 transmembrane helices grouped around a
translocation pathway that is closed to the cytoplasm by
a gate region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 30.1 bits (69), Expect = 5.3
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 185 VAIVGKPN-VGKSTLINSLLGENR 207
V I+G PN GKSTL+ +L G +
Sbjct: 28 VGILG-PNGAGKSTLLKTLAGLLK 50
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 30.5 bits (69), Expect = 5.4
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 11/61 (18%)
Query: 188 VGKPNVGKSTLINSLLGENRVITYDTPG-------TTRDSIKSLFEYNNKKYILIDTAGI 240
G+ VGKS+LIN+L + D TT LF ++ ++ DT G
Sbjct: 126 AGQSGVGKSSLINALDPSVKQQVNDISSKLGLGKHTTTHVE--LFHFHGG--LIADTPGF 181
Query: 241 R 241
Sbjct: 182 N 182
>gnl|CDD|173541 PTZ00348, PTZ00348, tyrosyl-tRNA synthetase; Provisional.
Length = 682
Score = 31.0 bits (70), Expect = 5.4
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 862 ACGQLSGEETDIVKKEMYSFIDELNGDNLSLRPEGTASVIRSVIENNLIYDGPKRLWYS 920
A +++GEE DI S E+N L+ G S ++ V EN +I P W S
Sbjct: 421 ASDEITGEEKDI------SAALEVNC--ALLKAYGLPSEVKIVRENEVILGNPNDFWVS 471
>gnl|CDD|223803 COG0731, COG0731, Fe-S oxidoreductases [Energy production and
conversion].
Length = 296
Score = 30.3 bits (69), Expect = 5.8
Identities = 39/183 (21%), Positives = 72/183 (39%), Gaps = 18/183 (9%)
Query: 626 CAINCIFCSTGRQGFVRNLTVGEIIGQLWVTEFKLRREKNIKINSQGKR--QITNIVMMG 683
C+ NC++C +G + T ++ E + E + + +G + ++ +
Sbjct: 34 CSYNCVYCW---RGRTKKGTPER---PEFIVEESILEELKLLLGYKGDEATEPDHVTISL 87
Query: 684 MGEPLLNYKSTIGALKLILSDHAYGLSRRHVILSTSGIIPMIDKLAQECPVELAVSLHAS 743
GEP L Y + +G +LI G L T+G +P + + + P +L VSL A
Sbjct: 88 SGEPTL-YPN-LG--ELIEEIKKRGKKT--TFLVTNGSLPDVLEELKL-PDQLYVSLDAP 140
Query: 744 NNNLRNKLV-PISKKYPLKELILACHRYITYSPRHMITFEYCMLHGINDTDIHAIELISL 802
+ ++ P K E IL + ++ GIND + E L
Sbjct: 141 DEKTFRRINRPHKKDS--WEKILEGLEIFRSEYKGRTVIRTTLVKGINDDEEELEEYAEL 198
Query: 803 MRK 805
+ +
Sbjct: 199 LER 201
>gnl|CDD|218141 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears to
be involved in plant resistance to bacteria.
Length = 211
Score = 29.9 bits (68), Expect = 5.8
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 188 VGKPNVGKSTLINSLLGENRVIT-YDTPGTTRDSIKSLFEYNNKKYILIDTAGI 240
VGK GKS NS+LG + G T+ ++ + +IDT G+
Sbjct: 6 VGKTGNGKSATGNSILGRKAFESKLRAQGVTKTCQLVSRTWDGRIINVIDTPGL 59
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 30.2 bits (69), Expect = 6.7
Identities = 27/93 (29%), Positives = 36/93 (38%), Gaps = 31/93 (33%)
Query: 184 KVAIVGKPNVGKSTLI-------NSLLGENRV--ITYDT------------------PGT 216
VA+VG VGK+T + L G+ +V IT DT P
Sbjct: 223 VVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVE 282
Query: 217 TRDSIKSLFE----YNNKKYILIDTAGIRRRNK 245
K L + + ILIDTAG +R+K
Sbjct: 283 VVYDPKELAKALEQLRDCDVILIDTAGRSQRDK 315
>gnl|CDD|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 29.9 bits (68), Expect = 6.8
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 184 KVAIVGKPNVGKSTLINSLLGENRV 208
V + G P VGK+T++N L + +
Sbjct: 4 VVVVTGVPGVGKTTVLNKALEKLKE 28
>gnl|CDD|220739 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling protein
DNA-binding domain. The plasmid conjugative coupling
protein TrwB forms hexamers from six structurally very
similar protomers. This hexamer contains a central
channel running from the cytosolic pole (made up by the
AADs) to the membrane pole ending at the transmembrane
pore shaped by 12 transmembrane helices, rendering an
overall mushroom-like structure. The TrwB_AAD (all-alpha
domain) domain appears to be the DNA-binding domain of
the structure. TrwB, a basic integral inner-membrane
nucleoside-triphosphate-binding protein, is the
structural prototype for the type IV secretion system
coupling proteins, a family of proteins essential for
macromolecular transport between cells and export.
Length = 386
Score = 30.2 bits (69), Expect = 6.8
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 5/36 (13%)
Query: 186 AIVGKPNVGKSTLINSLLGE-----NRVITYDTPGT 216
IVG GK+ + LL + +R I YD GT
Sbjct: 19 LIVGTTGTGKTQALRELLDQIRARGDRAIIYDPTGT 54
>gnl|CDD|225011 COG2100, COG2100, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 414
Score = 30.1 bits (68), Expect = 7.4
Identities = 45/190 (23%), Positives = 74/190 (38%), Gaps = 20/190 (10%)
Query: 612 EKNRNTLCISTQVGCAINCIFCST--GRQGFVRNLTVGEIIGQLWVTEFKLRREKNIKIN 669
++ N + + GC +NCIFCS G R L L K+ R K +
Sbjct: 103 DRGTNVIQVRPSTGCNLNCIFCSVDEGPYSRTRKLDYVVDPEYLLEWFEKVARFKGKGLE 162
Query: 670 SQGKRQITNIVMMGMGEPLLNYKST--IGALKLILSDHAYGLSRRHVILSTSGIIPMIDK 727
+ + G GEPLL + ALK + V+LS ++D+
Sbjct: 163 AH---------LDGQGEPLLYPHLVDLVQALKEHKGVEVVSMQTNGVLLSKK----LVDE 209
Query: 728 LAQECPVELAVSLHASNNNLRNKLVPISKKYPLKELILACHRYITYSPRHMITFEYCMLH 787
L + + +S+ A + L L K Y +K+ +L YI + ++ L
Sbjct: 210 LEEAGLDRINLSVDALDPKLAKMLAGR-KDYDVKK-VLEVAEYIANAGIDVL-IAPVWLP 266
Query: 788 GINDTDIHAI 797
G+ND ++ I
Sbjct: 267 GVNDDEMPKI 276
>gnl|CDD|197556 smart00178, SAR, Sar1p-like members of the Ras-family of small
GTPases. Yeast SAR1 is an essential gene required for
transport of secretory proteins from the endoplasmic
reticulum to the Golgi apparatus.
Length = 184
Score = 29.5 bits (66), Expect = 7.6
Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 15/88 (17%)
Query: 5 LVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYIGKKSFIIIDTGGFEPEV 64
++ +G N GK+TL + L N R L + P T+ E IG F D GG
Sbjct: 20 ILFLGLDNAGKTTLLHMLKNDR--LAQHQP--TQHPTSEELAIGNIKFTTFDLGG----- 70
Query: 65 KKGIMHEMTKQT-KQAIIESDIIIFIVD 91
H+ ++ K E + I+++VD
Sbjct: 71 -----HQQARRLWKDYFPEVNGIVYLVD 93
>gnl|CDD|213200 cd03233, ABCG_PDR_domain1, First domain of the pleiotropic drug
resistance-like subfamily G of ATP-binding cassette
transporters. The pleiotropic drug resistance (PDR) is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. This PDR subfamily represents
domain I of its (ABC-IM)2 organization. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds
including sugars, ions, peptides, and more complex
organic molecules. The nucleotide-binding domain shows
the highest similarity between all members of the
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 202
Score = 29.5 bits (67), Expect = 7.7
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 6/45 (13%)
Query: 1 MKP--VLVLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYG 43
+KP +++++GRP G STL L N + + D HY
Sbjct: 30 VKPGEMVLVLGRPGSGCSTLLKALANRTEG----NVSVEGDIHYN 70
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 29.2 bits (66), Expect = 7.8
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 178 HSIEYIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDT 237
EY KV IVG N GK+T++ L V T T G+ + Y N ++++ D
Sbjct: 12 PRKEY-KVIIVGLDNAGKTTILYQFLLGEVVHTSPTIGSNVEE----IVYKNIRFLMWDI 66
Query: 238 AG 239
G
Sbjct: 67 GG 68
>gnl|CDD|233723 TIGR02094, more_P_ylases, alpha-glucan phosphorylases. This family
consists of known phosphorylases, and homologs believed
to share the function of using inorganic phosphate to
cleave an alpha 1,4 linkage between the terminal glucose
residue and the rest of the polymer (maltodextrin,
glycogen, etc.). The name of the glucose storage polymer
substrate, and therefore the name of this enzyme, depends
on the chain lengths and branching patterns. A number of
the members of this family have been shown to operate on
small maltodextrins, as may be obtained by utilization of
exogenous sources. This family represents a distinct
clade from the related family modeled by
TIGR02093/pfam00343.
Length = 601
Score = 30.4 bits (69), Expect = 7.9
Identities = 10/38 (26%), Positives = 18/38 (47%)
Query: 991 DLINYIKKHKDSKWFCEDIKHSLYLNSLRVLDSKNLII 1028
LI+YI++ +W ++ + + R LD L I
Sbjct: 355 RLIDYIRRRLRERWLRRGADAAILMATDRFLDPDVLTI 392
>gnl|CDD|224930 COG2019, AdkA, Archaeal adenylate kinase [Nucleotide transport and
metabolism].
Length = 189
Score = 29.7 bits (67), Expect = 8.1
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 184 KVAIVGKPNVGKSTLINSLLGE 205
V I G P VGK+T++ L E
Sbjct: 6 VVVITGVPGVGKTTVLKIALKE 27
>gnl|CDD|236865 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 30.2 bits (69), Expect = 8.8
Identities = 11/20 (55%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 184 KVAIVGKPNVGKSTLINSLL 203
KVA++G+ GKSTL+ LL
Sbjct: 368 KVALLGRTGCGKSTLL-QLL 386
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras
and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in a
significant fraction of human cancers. Many Ras guanine
nucleotide exchange factors (GEFs) have been identified.
They are sequestered in the cytosol until activation by
growth factors triggers recruitment to the plasma
membrane or Golgi, where the GEF colocalizes with Ras.
Active (GTP-bound) Ras interacts with several effector
proteins that stimulate a variety of diverse cytoplasmic
signaling activities. Some are known to positively
mediate the oncogenic properties of Ras, including Raf,
phosphatidylinositol 3-kinase (PI3K), RalGEFs, and
Tiam1. Others are proposed to play negative regulatory
roles in oncogenesis, including RASSF and NORE/MST1.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 162
Score = 28.9 bits (65), Expect = 9.2
Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 181 EYIKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYIL--IDTA 238
EY K+ +VG VGKS L L+ + V YD T DS + + + +L +DTA
Sbjct: 1 EY-KLVVVGAGGVGKSALTIQLIQNHFVDEYDP--TIEDSYRKQVVIDGETCLLDILDTA 57
Query: 239 G 239
G
Sbjct: 58 G 58
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 28.7 bits (65), Expect = 9.3
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 11/63 (17%)
Query: 185 VAIVGKPNVGKSTL----INSLLGENRV-ITYDTPGTTR----DSIKSLFE--YNNKKYI 233
+ I G VGK+TL + LL EN + I D P R D ++ + KKY+
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSENILYINLDDPRFLRLALLDLLEEFLKLLLPGKKYL 64
Query: 234 LID 236
+D
Sbjct: 65 FLD 67
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.139 0.406
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 64,751,981
Number of extensions: 6711775
Number of successful extensions: 7868
Number of sequences better than 10.0: 1
Number of HSP's gapped: 7508
Number of HSP's successfully gapped: 435
Length of query: 1250
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1142
Effective length of database: 6,147,370
Effective search space: 7020296540
Effective search space used: 7020296540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 65 (28.5 bits)