RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17089
(419 letters)
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 555 bits (1432), Expect = 0.0
Identities = 198/419 (47%), Positives = 281/419 (67%), Gaps = 10/419 (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 TSRITRALISAIKNHPPCRKKLIRPKLRYAHQGGKNPPIIVIHGNRLKYIGNDYKRYLE 419
TS + R L A++ HPP K R K++YA Q G NPP V+ N + + YKRYLE
Sbjct: 352 TSVLNRVLEEAVERHPPPLVKGRRLKIKYATQVGTNPPTFVLFVNDPELLPFSYKRYLE 410
>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 = 544 bits (1405), Expect = 0.0
Identities = 197/418 (47%), Positives = 280/418 (66%), Gaps = 10/418 (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 SRITRALISAIKNHPPCRKKLIRPKLRYAHQGGKNPPIIVIHGNRLKYIGNDYKRYLE 419
S++ R L A+ HPP R K++YA Q G NPP V+ GNR + + YKRYLE
Sbjct: 353 SKLNRVLEEAVAAHPPPLVNGRRLKIKYATQVGTNPPTFVLFGNRPELLPFSYKRYLE 410
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 477 bits (1229), Expect = e-167
Identities = 188/422 (44%), Positives = 271/422 (64%), Gaps = 9/422 (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 LE 419
LE
Sbjct: 416 LE 417
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 292 bits (748), Expect = 4e-92
Identities = 139/424 (32%), Positives = 234/424 (55%), Gaps = 23/424 (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 RYLE 419
R+LE
Sbjct: 682 RFLE 685
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 280 bits (719), Expect = 2e-90
Identities = 149/429 (34%), Positives = 241/429 (56%), Gaps = 31/429 (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 GNDYKRYLE 419
Y+R+LE
Sbjct: 438 EAGYRRFLE 446
>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 = 237 bits (607), Expect = 2e-77
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 = 101 bits (254), Expect = 2e-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|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 = 219 bits (561), Expect = 8e-71
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 = 128 bits (324), Expect = 1e-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|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 = 120 bits (302), 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 = 114 bits (287), Expect = 7e-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 = 121 bits (305), Expect = 6e-33
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 = 101 bits (254), 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|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 121 bits (306), Expect = 2e-30
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 = 102 bits (256), Expect = 9e-24
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|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 117 bits (296), Expect = 5e-29
Identities = 51/122 (41%), Positives = 77/122 (63%), Gaps = 5/122 (4%)
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 WD 304
D
Sbjct: 331 AD 332
Score = 105 bits (264), Expect = 9e-25
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 = 106 bits (267), Expect = 2e-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 = 100 bits (251), Expect = 3e-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|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 100 bits (252), Expect = 5e-24
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 = 93.2 bits (233), Expect = 2e-21
Identities = 49/165 (29%), Positives = 80/165 (48%), Gaps = 19/165 (11%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDR-----HYGEGYIGKKSFIIIDTGG-F 60
+VGRPNVGKSTL N L + ++V+ P TR R + I I +DT G
Sbjct: 10 IVGRPNVGKSTLLNALVGQKISIVSPKPQTTRHRIRGIVTEDDAQI-----IFVDTPGIH 64
Query: 61 EPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINK 120
+P K+ + M K ++ + D+++F+VD + + D+ I L+K P++LV+NK
Sbjct: 65 KP--KRALNRAMNKAAWSSLKDVDLVLFVVDADEKIGPGDEFILEKLKKVKTPVILVLNK 122
Query: 121 SENINSSISL----DFYELGIGNPHI--ISALYGNGIKNFLENIL 159
+ + L + + I ISAL G+ + L+ I
Sbjct: 123 IDLVKDKEELLPLLEELSELMDFAEIVPISALKGDNVDELLDVIA 167
>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 = 102 bits (255), Expect = 9e-24
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 = 77.5 bits (191), Expect = 2e-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|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 = 95.6 bits (239), 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
Score = 95.6 bits (239), Expect = 2e-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
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 98.0 bits (245), Expect = 4e-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 = 96.9 bits (242), Expect = 1e-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|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 = 94.0 bits (234), Expect = 8e-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 = 73.9 bits (182), Expect = 1e-15
Identities = 42/127 (33%), Positives = 65/127 (51%), Gaps = 9/127 (7%)
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 NKSENIN 125
NK + +
Sbjct: 117 NKIDLRD 123
>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 = 85.6 bits (212), Expect = 7e-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 = 85.2 bits (211), 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|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 = 88.6 bits (220), Expect = 7e-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 = 77.4 bits (191), Expect = 5e-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|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 = 85.6 bits (213), Expect = 2e-18
Identities = 50/166 (30%), Positives = 82/166 (49%), Gaps = 18/166 (10%)
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 TGGFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVL 116
T G + E + G ++T++ + ++D+ + +VD G E + + L++ P ++
Sbjct: 62 TAGLDDEGELG--ELRVEKTREVLDKTDLALLVVDAGVGPGEYELELIEELKERKIPYIV 119
Query: 117 VINKSENINSSISLDFYELGIGNPHI-ISALYGNGIKNFLENILTI 161
VINK + S L+ E G P I +SAL G GI E I+ +
Sbjct: 120 VINKIDLGEESAELEKLEKKFGLPPIFVSALTGEGIDELKEAIIEL 165
Score = 77.6 bits (192), Expect = 1e-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|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 = 76.0 bits (188), Expect = 2e-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 = 52.1 bits (126), Expect = 3e-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|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 = 72.9 bits (180), Expect = 3e-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 = 62.1 bits (152), Expect = 2e-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|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 = 71.0 bits (175), 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 = 53.6 bits (130), Expect = 2e-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|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 73.1 bits (180), Expect = 7e-14
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 = 58.8 bits (143), Expect = 2e-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|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 = 68.7 bits (169), 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 = 48.7 bits (117), Expect = 7e-07
Identities = 20/31 (64%), Positives = 22/31 (70%)
Query: 8 VGRPNVGKSTLFNRLTNSRDALVANYPGLTR 38
VG PNVGKSTL NRL + A V N PG+TR
Sbjct: 121 VGIPNVGKSTLINRLRGKKVAKVGNKPGVTR 151
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 70.4 bits (173), Expect = 3e-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 = 42.6 bits (101), Expect = 2e-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 = 68.2 bits (167), Expect = 1e-12
Identities = 52/186 (27%), Positives = 88/186 (47%), Gaps = 13/186 (6%)
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 GIRRRN 244
GI
Sbjct: 186 GIIPPK 191
Score = 49.7 bits (119), Expect = 1e-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|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 = 66.8 bits (164), Expect = 2e-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 = 46.7 bits (112), Expect = 9e-06
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 = 67.8 bits (166), Expect = 3e-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 = 53.2 bits (128), Expect = 2e-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|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 = 63.6 bits (155), Expect = 4e-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 = 34.3 bits (79), Expect = 0.040
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 = 64.2 bits (157), 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 = 37.6 bits (88), Expect = 0.005
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|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 65.6 bits (161), Expect = 6e-12
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 = 45.9 bits (110), Expect = 1e-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|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 62.6 bits (153), Expect = 2e-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 = 61.9 bits (151), Expect = 3e-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|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 = 61.3 bits (150), Expect = 4e-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 = 49.8 bits (120), Expect = 4e-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|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 = 63.4 bits (155), Expect = 5e-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|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 60.5 bits (148), Expect = 1e-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 = 50.5 bits (122), Expect = 2e-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|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 = 58.6 bits (143), Expect = 5e-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 = 46.3 bits (111), Expect = 7e-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|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 = 9e-10
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 = 0.014
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 = 57.5 bits (140), Expect = 4e-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 = 39.8 bits (94), Expect = 0.002
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 = 54.2 bits (131), 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 = 46.1 bits (110), 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 = 53.6 bits (129), 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 = 44.7 bits (106), Expect = 2e-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 = 53.7 bits (130), Expect = 1e-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 = 39.5 bits (93), Expect = 0.001
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|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 = 52.9 bits (128), Expect = 2e-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 = 41.4 bits (98), Expect = 2e-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 = 54.7 bits (131), Expect = 3e-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 = 43.2 bits (101), Expect = 2e-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 = 54.2 bits (131), Expect = 4e-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 = 39.6 bits (93), Expect = 0.002
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|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 = 51.9 bits (125), Expect = 4e-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 = 33.8 bits (78), Expect = 0.064
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|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 53.2 bits (129), Expect = 9e-08
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 = 34.3 bits (80), Expect = 0.10
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 185 VAIVGKPNVGKSTLINSL 202
V +VG PN GKSTLI+++
Sbjct: 161 VGLVGLPNAGKSTLISAV 178
>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 = 49.3 bits (119), Expect = 4e-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 = 37.4 bits (88), Expect = 0.005
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 185 VAIVGKPNVGKSTLINSL 202
V +VG PN GKSTL++++
Sbjct: 3 VGLVGLPNAGKSTLLSAI 20
>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 = 5e-07
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 = 2e-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|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 51.1 bits (123), Expect = 5e-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 = 40.3 bits (95), Expect = 0.001
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|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 = 50.2 bits (121), Expect = 5e-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 = 38.3 bits (90), Expect = 0.004
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|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 50.6 bits (122), Expect = 6e-07
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 = 41.4 bits (98), Expect = 6e-04
Identities = 14/20 (70%), Positives = 17/20 (85%)
Query: 183 IKVAIVGKPNVGKSTLINSL 202
+K+ IVG PNVGKSTL N+L
Sbjct: 3 LKIGIVGLPNVGKSTLFNAL 22
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 50.4 bits (122), Expect = 7e-07
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 = 38.5 bits (91), Expect = 0.005
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 = 49.9 bits (120), Expect = 9e-07
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 = 36.4 bits (85), Expect = 0.019
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|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 = 49.0 bits (118), Expect = 1e-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 = 0.071
Identities = 13/16 (81%), Positives = 14/16 (87%)
Query: 187 IVGKPNVGKSTLINSL 202
IVG PNVGKSTL N+L
Sbjct: 3 IVGLPNVGKSTLFNAL 18
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 49.5 bits (119), Expect = 1e-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 = 31.0 bits (71), Expect = 1.2
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|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 = 47.6 bits (114), Expect = 2e-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 = 41.0 bits (97), Expect = 3e-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|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 48.3 bits (116), Expect = 4e-06
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 = 0.007
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 183 IKVAIVGKPNVGKSTLINS 201
I + +VGKPNVGKST N+
Sbjct: 2 ITIGLVGKPNVGKSTFFNA 20
>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 = 47.8 bits (115), Expect = 5e-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 = 37.4 bits (88), Expect = 0.011
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 185 VAIVGKPNVGKSTLINSL 202
V +VG PN GKSTLI+++
Sbjct: 160 VGLVGLPNAGKSTLISAV 177
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 45.3 bits (108), Expect = 1e-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 = 40.3 bits (95), Expect = 6e-04
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|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 46.4 bits (111), Expect = 2e-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 = 0.046
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 = 45.0 bits (106), Expect = 2e-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 = 41.9 bits (98), Expect = 3e-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|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 45.7 bits (109), Expect = 3e-05
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
Score = 29.5 bits (67), Expect = 3.1
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 5 LVLVGRPNVGKSTLFNRL 22
+ L+G VGKSTL N L
Sbjct: 198 VALLGSSGVGKSTLVNAL 215
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 45.9 bits (109), Expect = 3e-05
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
Score = 28.9 bits (65), Expect = 6.4
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 185 VAIVGKPNVGKSTLINSLLG 204
+ ++G PN GK+TL N L G
Sbjct: 6 IGLIGNPNSGKTTLFNQLTG 25
>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 = 44.0 bits (105), Expect = 3e-05
Identities = 41/186 (22%), Positives = 73/186 (39%), Gaps = 35/186 (18%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRD------------SIKS---LFEYNN 229
+ I+G + GK+TL ++LL I+ ++ R +IK FE
Sbjct: 6 IGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVSFETKK 65
Query: 230 KKYILIDTAGIRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANFI 289
+ +IDT G + T E+I S A+ IL++DA + + Q
Sbjct: 66 RLINIIDTPG--HVDFTKEMIRGASQ---------ADGAILVVDAVEGVMPQTREHLLLA 114
Query: 290 YESGRSLIVCVNKWDSIIHNQRKIIKNNIKKKLNFLSFAMFN-------FISAIKLNNIN 342
G +IV +NK D + + + + I ++ L F SA+ I+
Sbjct: 115 KTLGVPIIVFINKIDRVDDAELEEVVEEISRE--LLEKYGFGGETVPVVPGSALTGEGID 172
Query: 343 SFMESI 348
+E++
Sbjct: 173 ELLEAL 178
Score = 42.9 bits (102), Expect = 7e-05
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|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 = 43.9 bits (105), Expect = 4e-05
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|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 44.8 bits (106), Expect = 4e-05
Identities = 32/159 (20%), Positives = 59/159 (37%), Gaps = 21/159 (13%)
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---------WDSIIHNQRKIIKNNIKKKLNFL 325
++ V + WDS H IK I++K L
Sbjct: 151 VLFVVTQADRAEPGREWDSAGHQPSPAIKQFIEEKAEAL 189
Score = 41.7 bits (98), Expect = 4e-04
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|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 = 43.7 bits (104), Expect = 5e-05
Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 26/119 (21%)
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 NFLRKSGQPIVLVINK------SENINSSISLDFYEL--GIGNPHI----ISALYGNGI 151
+ L + +V+ +NK E + I D+ +G I ISAL G+ +
Sbjct: 127 SLLGI--RHVVVAVNKMDLVDYDEEVFEEIKADYLAFAASLGIEDITFIPISALEGDNV 183
Score = 31.0 bits (71), Expect = 0.75
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|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 = 40.5 bits (95), Expect = 2e-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 = 35.5 bits (82), Expect = 0.011
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 = 42.0 bits (99), Expect = 4e-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 = 41.8 bits (99), Expect = 5e-04
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 = 31.4 bits (72), Expect = 0.82
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 = 41.6 bits (99), Expect = 5e-04
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 = 37.0 bits (87), Expect = 0.015
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 = 41.5 bits (98), Expect = 5e-04
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 = 35.3 bits (82), Expect = 0.046
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 = 40.4 bits (95), Expect = 0.001
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 = 32.3 bits (74), Expect = 0.41
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|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 39.1 bits (92), Expect = 0.001
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 = 32.9 bits (76), Expect = 0.12
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|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 = 38.8 bits (91), Expect = 0.001
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 = 32.7 bits (75), Expect = 0.14
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|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 39.6 bits (93), Expect = 0.002
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|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 = 38.2 bits (90), Expect = 0.003
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|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 = 38.1 bits (89), Expect = 0.003
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 = 31.9 bits (73), Expect = 0.39
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|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 38.9 bits (91), Expect = 0.004
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
Score = 29.7 bits (67), Expect = 2.9
Identities = 36/126 (28%), Positives = 60/126 (47%), Gaps = 11/126 (8%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNN-KKYILIDTAGIRRR 243
V++VG N GKSTL N + E RV D T D + + + +L DT G R
Sbjct: 200 VSLVGYTNAGKSTLFNRIT-EARVYAADQLFATLDPTLRRIDVADVGETVLADTVGF-IR 257
Query: 244 NKTFEVIEKFSVIKTLKSILEANVVILLLDA-----QQNISAQDINIANFIYESGRSLIV 298
+ +++ F TL+ +A +++ ++DA Q+NI A + + +L+V
Sbjct: 258 HLPHDLVAAFKA--TLQETRQATLLLHVVDAADVRVQENIEAVNTVLEEIDAHEIPTLLV 315
Query: 299 CVNKWD 304
+NK D
Sbjct: 316 -MNKID 320
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 38.8 bits (91), Expect = 0.004
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
Score = 28.0 bits (63), Expect = 9.8
Identities = 44/180 (24%), Positives = 67/180 (37%), Gaps = 72/180 (40%)
Query: 194 GKSTLINSLLGENRVITYDTPGTTRDSIKSL----------------------------- 224
GKSTLI LL YDT D + SL
Sbjct: 18 GKSTLIGRLL-------YDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDGLEAEREQ 70
Query: 225 ----------FEYNNKKYILIDTAGIRR--RNKTFEVIEKFSVIKTLKSILEANVVILLL 272
F +K+I+ DT G + RN + T S A++ ILL+
Sbjct: 71 GITIDVAYRYFSTEKRKFIIADTPGHEQYTRN-----------MATGAS--TADLAILLV 117
Query: 273 DAQQNISAQDIN---IANFIYESG-RSLIVCVNKWDSIIHNQRKIIKNNIKKKLNFLSFA 328
DA++ + Q IA+ + G R ++V VNK D + +++ I ++L+FA
Sbjct: 118 DARKGVLEQTRRHSFIASLL---GIRHVVVAVNKMDLVDYSEEVF--EAIVA--DYLAFA 170
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 38.3 bits (90), Expect = 0.007
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|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 = 36.9 bits (86), Expect = 0.008
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|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 = 37.4 bits (87), Expect = 0.012
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 = 29.3 bits (66), Expect = 4.0
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|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 = 35.9 bits (84), Expect = 0.019
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|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 = 35.2 bits (82), Expect = 0.020
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 = 33.7 bits (78), Expect = 0.087
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|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 = 34.9 bits (80), Expect = 0.025
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 = 34.9 bits (81), Expect = 0.036
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 = 34.6 bits (80), Expect = 0.044
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGE 205
+++ ++G VGKS+LI SL+ E
Sbjct: 3 VRIVLIGDEGVGKSSLIMSLVSE 25
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 35.3 bits (82), Expect = 0.055
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 = 0.058
Identities = 10/21 (47%), Positives = 17/21 (80%)
Query: 184 KVAIVGKPNVGKSTLINSLLG 204
++A+VG GK++L+N+LLG
Sbjct: 378 RIALVGPSGAGKTSLLNALLG 398
>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 = 35.3 bits (82), Expect = 0.059
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 184 KVAIVGKPNVGKSTLINSLLG 204
+VA+VG GKSTL+N LLG
Sbjct: 350 RVALVGPSGAGKSTLLNLLLG 370
>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 = 0.093
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|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 = 0.11
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|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 = 0.11
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 = 33.0 bits (76), Expect = 0.22
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|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 = 33.5 bits (77), Expect = 0.13
Identities = 13/19 (68%), Positives = 15/19 (78%)
Query: 185 VAIVGKPNVGKSTLINSLL 203
V +VG P VGKSTLI SL+
Sbjct: 42 VVVVGPPGVGKSTLIRSLI 60
>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 = 32.8 bits (76), Expect = 0.14
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|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 33.3 bits (77), Expect = 0.20
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|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 = 32.6 bits (75), Expect = 0.24
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|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 = 32.7 bits (75), Expect = 0.24
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|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 = 32.4 bits (74), Expect = 0.25
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 = 32.0 bits (73), Expect = 0.36
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|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 33.4 bits (77), Expect = 0.25
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|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 = 31.7 bits (73), Expect = 0.28
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 184 KVAIVGKPNVGKSTLINSLLGE 205
++ +VG+ GKSTL+ + GE
Sbjct: 28 RIGLVGRNGAGKSTLLKLIAGE 49
>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 = 32.8 bits (75), Expect = 0.30
Identities = 17/31 (54%), Positives = 18/31 (58%)
Query: 7 LVGRPNVGKSTLFNRLTNSRDALVANYPGLT 37
+VG PNVGKSTLF TN AN P T
Sbjct: 7 IVGLPNVGKSTLFAATTNLLGNEAANPPFTT 37
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 32.3 bits (74), Expect = 0.32
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|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 = 31.6 bits (72), Expect = 0.34
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|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 = 32.7 bits (75), Expect = 0.34
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 184 KVAIVGKPNVGKSTLINSLLG 204
KVAI+G+ GKSTL+ L G
Sbjct: 366 KVAILGRSGSGKSTLLQLLAG 386
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 32.9 bits (75), Expect = 0.37
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 = 31.7 bits (72), Expect = 0.83
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|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 = 31.4 bits (72), Expect = 0.40
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|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 31.4 bits (72), Expect = 0.46
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 184 KVAIVGKPNVGKSTLINSL 202
++ I G P+ GK+TL+ +L
Sbjct: 1 RIVITGGPSTGKTTLLEAL 19
>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 = 32.2 bits (74), Expect = 0.47
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|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 31.4 bits (72), Expect = 0.49
Identities = 10/22 (45%), Positives = 18/22 (81%)
Query: 185 VAIVGKPNVGKSTLINSLLGEN 206
+A+VG + GKS+++N+LLG +
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRD 22
>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 = 31.2 bits (72), Expect = 0.54
Identities = 13/21 (61%), Positives = 14/21 (66%)
Query: 184 KVAIVGKPNVGKSTLINSLLG 204
KVAIVG GKSTL+ LL
Sbjct: 30 KVAIVGPSGSGKSTLLKLLLR 50
>gnl|CDD|236515 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
Length = 332
Score = 32.1 bits (74), Expect = 0.55
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 183 IKVAIVGKPNVGKSTLINSL 202
+++ I G P VGKST I +L
Sbjct: 57 LRIGITGVPGVGKSTFIEAL 76
>gnl|CDD|237894 PRK15064, PRK15064, ABC transporter ATP-binding protein;
Provisional.
Length = 530
Score = 32.2 bits (74), Expect = 0.55
Identities = 11/22 (50%), Positives = 19/22 (86%)
Query: 184 KVAIVGKPNVGKSTLINSLLGE 205
++AI+G+ VGK+TL+ +L+GE
Sbjct: 347 RLAIIGENGVGKTTLLRTLVGE 368
>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 = 32.2 bits (73), Expect = 0.57
Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 8/93 (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--VILLLD 273
++ + + ++ ++K ++ N ++L +D
Sbjct: 177 KSSASDQSKNEKILSSVKKFIKKNPPDIVLYVD 209
>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 = 31.4 bits (72), Expect = 0.65
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 184 KVAIVGKPNVGKSTLINSLLG 204
VAIVG GK+TLIN L+
Sbjct: 31 TVAIVGPTGAGKTTLINLLMR 51
>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 = 0.66
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|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 31.5 bits (72), Expect = 0.67
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|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 = 0.68
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|226647 COG4181, COG4181, Predicted ABC-type transport system involved in
lysophospholipase L1 biosynthesis, ATPase component
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 228
Score = 31.2 bits (71), Expect = 0.68
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|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 = 30.9 bits (70), Expect = 0.69
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 = 0.70
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|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 = 0.73
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|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 32.0 bits (72), Expect = 0.75
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|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 31.8 bits (73), Expect = 0.77
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|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 29.9 bits (68), Expect = 0.85
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 = 28.4 bits (64), Expect = 2.8
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|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 = 30.5 bits (70), Expect = 0.87
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
Score = 27.4 bits (62), Expect = 9.5
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 5 LVLVGRPNVGKSTLFNRLTN 24
+VL+G VGK++L R +
Sbjct: 3 IVLIGDSGVGKTSLLLRFVD 22
>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 = 30.4 bits (68), Expect = 0.92
Identities = 17/94 (18%), Positives = 27/94 (28%), Gaps = 16/94 (17%)
Query: 184 KVAIVGKPNVGKSTLINSLLGE----NRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAG 239
+ IVG P GK+TL +L E + Y + + +G
Sbjct: 4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSG 63
Query: 240 IRRRNKTFEVIEKFSVIKTLKSILEANVVILLLD 273
R + K +L+LD
Sbjct: 64 ELRLRLALALARKL------------KPDVLILD 85
>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 = 31.5 bits (72), Expect = 1.00
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|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 = 30.0 bits (68), Expect = 1.0
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|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 = 30.6 bits (70), Expect = 1.1
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|237422 PRK13548, hmuV, hemin importer ATP-binding subunit; Provisional.
Length = 258
Score = 30.9 bits (71), Expect = 1.2
Identities = 14/22 (63%), Positives = 17/22 (77%), Gaps = 2/22 (9%)
Query: 185 VAIVGKPN-VGKSTLINSLLGE 205
VAI+G PN GKSTL+ +L GE
Sbjct: 31 VAILG-PNGAGKSTLLRALSGE 51
>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 = 30.5 bits (70), Expect = 1.2
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 = 1.2
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|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 29.7 bits (67), Expect = 1.4
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 185 VAIVGKPNVGKSTLINSLL 203
V +VG + GK+TLI LL
Sbjct: 3 VLVVGPKDSGKTTLIRKLL 21
>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 = 30.2 bits (69), Expect = 1.5
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 184 KVAIVGKPNVGKSTLINSLL 203
KV IVG+ GKS+L+ +L
Sbjct: 32 KVGIVGRTGSGKSSLLLALF 51
>gnl|CDD|133356 cd04156, ARLTS1, Arf-like tumor suppressor gene 1 (ARLTS1 or
Arl11). ARLTS1 (Arf-like tumor suppressor gene 1), also
known as Arl11, is a member of the Arf family of small
GTPases that is believed to play a major role in
apoptotic signaling. ARLTS1 is widely expressed and
functions as a tumor suppressor gene in several human
cancers. ARLTS1 is a low-penetrance suppressor that
accounts for a small percentage of familial melanoma or
familial chronic lymphocytic leukemia (CLL). ARLTS1
inactivation seems to occur most frequently through
biallelic down-regulation by hypermethylation of the
promoter. In breast cancer, ARLTS1 alterations were
typically a combination of a hypomorphic polymorphism
plus loss of heterozygosity. In a case of thyroid
adenoma, ARLTS1 alterations were polymorphism plus
promoter hypermethylation. The nonsense polymorphism
Trp149Stop occurs with significantly greater frequency
in familial cancer cases than in sporadic cancer cases,
and the Cys148Arg polymorphism is associated with an
increase in high-risk familial breast cancer.
Length = 160
Score = 29.7 bits (67), Expect = 1.5
Identities = 33/125 (26%), Positives = 55/125 (44%), Gaps = 21/125 (16%)
Query: 5 LVLVGRPNVGKSTLFNRLTNSRDALVANYP--GLTRDRHYGEGYIGKKSFIIIDTGGFEP 62
++L+G + GKSTL +L + LV P G + E ++ S + D GG E
Sbjct: 2 VLLLGLDSAGKSTLLYKLKH--AELVTTIPTVGFNVEMLQLEKHL---SLTVWDVGGQEK 56
Query: 63 EVKKGIMHEMTKQTKQAIIESDIIIFIVDG--RQGLVEQDKLITNFLRK---SGQPIVLV 117
M K + +D ++++VD L E K + + L+ G P+VL+
Sbjct: 57 ---------MRTVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLL 107
Query: 118 INKSE 122
NK +
Sbjct: 108 ANKQD 112
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 30.4 bits (69), Expect = 1.6
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 222 KSLFEYNNKKYILIDTAG 239
++L +K ILIDTAG
Sbjct: 266 EALDRLRDKDLILIDTAG 283
>gnl|CDD|201353 pfam00625, Guanylate_kin, Guanylate kinase.
Length = 183
Score = 30.0 bits (68), Expect = 1.7
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 = 29.9 bits (68), Expect = 1.8
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|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 = 30.6 bits (69), Expect = 1.8
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|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 = 1.9
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|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 = 1.9
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|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 = 29.9 bits (67), Expect = 1.9
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|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 = 29.7 bits (68), Expect = 1.9
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|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 = 29.8 bits (68), Expect = 1.9
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|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 = 29.7 bits (67), Expect = 2.2
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|222927 PHA02774, PHA02774, E1; Provisional.
Length = 613
Score = 30.2 bits (69), Expect = 2.2
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 186 AIVGKPNVGKSTLINSLLG--ENRVITY 211
I G P+ GKS SL+ + +VI++
Sbjct: 438 VIYGPPDTGKSMFCMSLIKFLKGKVISF 465
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 30.2 bits (69), Expect = 2.2
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 185 VAIVGKPNVGKSTLINSL 202
V +VG P+ GKS+LI++L
Sbjct: 162 VGLVGFPSAGKSSLISAL 179
>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 = 2.3
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|236865 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 30.2 bits (69), Expect = 2.6
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|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 29.5 bits (67), Expect = 2.6
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|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 29.4 bits (67), Expect = 2.7
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|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 = 29.2 bits (66), Expect = 2.9
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|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 29.9 bits (68), Expect = 2.9
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|224930 COG2019, AdkA, Archaeal adenylate kinase [Nucleotide transport and
metabolism].
Length = 189
Score = 28.9 bits (65), Expect = 3.3
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|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 = 3.5
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 = 28.3 bits (64), Expect = 3.7
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
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 28.0 bits (62), Expect = 3.9
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 184 KVAIVGKPNVGKSTLINSL 202
+ I G P GKSTL L
Sbjct: 1 IILITGPPGSGKSTLAKKL 19
>gnl|CDD|234401 TIGR03925, T7SS_EccC_b, type VII secretion protein EccCb. This
model represents the C-terminal domain or EccCb subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 566
Score = 29.5 bits (67), Expect = 4.0
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 185 VAIVGKPNVGKSTLINSL 202
VAIVG P GKST + +L
Sbjct: 82 VAIVGGPQSGKSTALRTL 99
>gnl|CDD|239388 cd03114, ArgK-like, The function of this protein family is unkown.
The protein sequences are similar to the ArgK protein in
E. coli. ArgK protein is a membrane ATPase which is
required for transporting arginine, ornithine and lysine
into the cells by the arginine and ornithine (AO system)
and lysine, arginine and ornithine (LAO) transport
systems.
Length = 148
Score = 28.4 bits (64), Expect = 4.0
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 185 VAIVGKPNVGKSTLINSLLGENR 207
+ I G P GKSTLI++L+ R
Sbjct: 2 IGITGVPGAGKSTLIDALITALR 24
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 29.5 bits (67), Expect = 4.3
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 185 VAIVGKPNVGKSTLINSLLG 204
+ IVG+ GKSTL +L+G
Sbjct: 38 LGIVGESGSGKSTLALALMG 57
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 29.2 bits (66), Expect = 4.3
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYPG-LTRDRH 41
V+ G VGKS+L NRL + V G L R RH
Sbjct: 176 VVAGPSGVGKSSLINRLIPDVELRVGKVSGKLGRGRH 212
>gnl|CDD|213260 cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of
the nitrate and sulfonate transporters. NrtD and SsuB
are the ATP-binding subunits of the bacterial ABC-type
nitrate and sulfonate transport systems, respectively.
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 = 220
Score = 29.0 bits (66), Expect = 4.4
Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 21/61 (34%)
Query: 147 YGNGIKNF--LENI-LTIELPYKKFFKKKEFTNIHSIEYIKVAIVGKPNVGKSTLINSLL 203
YG G LE+I L++E + EF VA+VG GKSTL+ +
Sbjct: 10 YGGGGGAVTALEDISLSVE--------EGEF----------VALVGPSGCGKSTLLRIIA 51
Query: 204 G 204
G
Sbjct: 52 G 52
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to the
beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal extension
is reported to be conserved among the family and lack
the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 28.9 bits (65), Expect = 4.5
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 184 KVAIVGKPNVGKSTLINSLLGE 205
+V ++G VGKS+L N
Sbjct: 2 RVVLLGDSGVGKSSLANIFTAG 23
Score = 27.8 bits (62), Expect = 9.7
Identities = 30/125 (24%), Positives = 53/125 (42%), Gaps = 19/125 (15%)
Query: 6 VLVGRPNVGKSTLFNRLTNSRDALVANYPGLTRDRHYGEGYI---GKKS-FIIIDTGGFE 61
VL+G VGKS+L N T A E + G+++ ++ D
Sbjct: 4 VLLGDSGVGKSSLANIFTAGVYEDSAYEASGD---DTYERTVSVDGEEATLVVYDH---- 56
Query: 62 PEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQDKLITNFLRKSGQ----PIVLV 117
E + G + + + ++ +I++ V R + +L LR++ Q PI+LV
Sbjct: 57 WEQEDG---MWLEDSCMQVGDAYVIVYSVTDRSSFEKASELR-IQLRRARQAEDIPIILV 112
Query: 118 INKSE 122
NKS+
Sbjct: 113 GNKSD 117
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 28.3 bits (64), Expect = 4.5
Identities = 31/126 (24%), Positives = 54/126 (42%), Gaps = 29/126 (23%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSIKSLFEYNNKKYILIDTAG--- 239
+++ I+G N GK+T++ L V T T G ++++ Y N K+ + D G
Sbjct: 15 MRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFN---VETV-TYKNVKFTVWDVGGQES 70
Query: 240 IRR--RN---KTFEVI--------EKFSVIKT-LKSILE----ANVVILLL----DAQQN 277
+R RN T VI ++ K L ++L A+ +L+L D
Sbjct: 71 LRPLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELADAPLLILANKQDLPGA 130
Query: 278 ISAQDI 283
+S +I
Sbjct: 131 MSEAEI 136
>gnl|CDD|215692 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 28.2 bits (64), Expect = 4.7
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 5 LVLVGRPNVGKSTLFNRLTNSR 26
LVLVG VGKS+L R T ++
Sbjct: 2 LVLVGDGGVGKSSLLIRFTQNK 23
>gnl|CDD|206650 cd01851, GBP, Guanylate-binding protein (GBP) family (N-terminal
domain). Guanylate-binding protein (GBP), N-terminal
domain. Guanylate-binding proteins (GBPs) define a group
of proteins that are synthesized after activation of the
cell by interferons. The biochemical properties of GBPs
are clearly different from those of Ras-like and
heterotrimeric GTP-binding proteins. They bind guanine
nucleotides with low affinity (micromolar range), are
stable in their absence and have a high turnover GTPase.
In addition to binding GDP/GTP, they have the unique
ability to bind GMP with equal affinity and hydrolyze
GTP not only to GDP, but also to GMP. Furthermore, two
unique regions around the base and the phosphate-binding
areas, the guanine and the phosphate caps, respectively,
give the nucleotide-binding site a unique appearance not
found in the canonical GTP-binding proteins. The
phosphate cap, which constitutes the region analogous to
switch I, completely shields the phosphate-binding site
from solvent such that a potential GTPase-activating
protein (GAP) cannot approach.
Length = 224
Score = 28.8 bits (65), Expect = 4.7
Identities = 25/111 (22%), Positives = 43/111 (38%), Gaps = 16/111 (14%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVI-TYDTPGTTRDSI---KSLFEYNNKK---YILIDT 237
V++ G + GKS L+N L G + DT T I F+ + K +L+DT
Sbjct: 10 VSVFGSQSSGKSFLLNHLFGTSDGFDVMDTSQQTTKGIWMWSDPFKDTDGKKHAVLLLDT 69
Query: 238 AGIRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDAQQNISAQDINIANF 288
G R + E + + + L ++V+I N+ +
Sbjct: 70 EGTDGRERGEF--ENDARL-FALATLLSSVLIY------NMWQTILGDDLD 111
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 29.1 bits (66), Expect = 4.7
Identities = 14/21 (66%), Positives = 16/21 (76%)
Query: 184 KVAIVGKPNVGKSTLINSLLG 204
KVAIVG+ GKSTL+ LLG
Sbjct: 501 KVAIVGRSGSGKSTLLKLLLG 521
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 29.1 bits (66), Expect = 4.8
Identities = 34/119 (28%), Positives = 51/119 (42%), Gaps = 33/119 (27%)
Query: 49 KKSFIIIDTGGFEPEVKKGIMHEM-TKQTKQAIIESDIIIFIVDGRQGLVEQDK---LIT 104
K+ FII DT G HE T+ D+ I ++D R+G+++Q + I
Sbjct: 106 KRKFIIADTPG----------HEQYTRNMATGASTCDLAILLIDARKGVLDQTRRHSFIA 155
Query: 105 NFLRKSG-QPIVLVINK------SENINSSISLDFYE----LGIGNPHI----ISALYG 148
L G + +V+ +NK SE + I D+ L GN I +SAL G
Sbjct: 156 TLL---GIKHLVVAVNKMDLVDYSEEVFERIREDYLTFAEQLP-GNLDIRFVPLSALEG 210
>gnl|CDD|234208 TIGR03436, acidobact_VWFA, VWFA-related Acidobacterial domain.
Members of this family are bacterial domains that
include a region related to the von Willebrand factor
type A (VWFA) domain (pfam00092). These domains are
restricted to, and have undergone a large paralogous
family expansion in, the Acidobacteria, including
Solibacter usitatus and Acidobacterium capsulatum ATCC
51196.
Length = 296
Score = 28.8 bits (65), Expect = 4.9
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 8/61 (13%)
Query: 40 RHYGEGYIGKKSFIIIDTGGFEPEVKKGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQ 99
G G+K+ I+I + G + + + + A +D+ I+ +D R GL
Sbjct: 157 NALA-GIPGRKALIVI-SDGGDNRSRDTLE-----RAIDAAQRADVAIYSIDAR-GLRAP 208
Query: 100 D 100
D
Sbjct: 209 D 209
>gnl|CDD|182123 PRK09866, PRK09866, hypothetical protein; Provisional.
Length = 741
Score = 29.0 bits (65), Expect = 5.1
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 13/55 (23%)
Query: 173 EFTNIHSIEYIKVAIVGKPNVGKSTLINSLLG------ENRVIT------YDTPG 215
E I +E + +AIVG GKST IN+++G NR +T TPG
Sbjct: 61 ELRKISRLEMV-LAIVGTMKAGKSTTINAIVGTEVLPNRNRPMTALPTLIRHTPG 114
>gnl|CDD|236151 PRK08099, PRK08099, bifunctional DNA-binding transcriptional
repressor/ NMN adenylyltransferase; Provisional.
Length = 399
Score = 28.9 bits (65), Expect = 5.4
Identities = 32/111 (28%), Positives = 41/111 (36%), Gaps = 41/111 (36%)
Query: 132 FYELGIGN-PHIISALYGNGIKNFLEN-------ILTIEL----PYKKFF--------KK 171
F E G+ PH + NGIK F+ I T E Y++ K
Sbjct: 130 FNEEGMEPYPHGWDV-WSNGIKAFMAEKGIQPDVIYTSEEQDAPQYEEHLGIETVLVDPK 188
Query: 172 KEFTNI----------HSIEYI----------KVAIVGKPNVGKSTLINSL 202
+ F NI EYI VAI+G + GKSTL+N L
Sbjct: 189 RTFMNISGTQIRENPFRYWEYIPTEVRPFFVRTVAILGGESSGKSTLVNKL 239
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 29.3 bits (66), Expect = 5.6
Identities = 12/21 (57%), Positives = 17/21 (80%)
Query: 185 VAIVGKPNVGKSTLINSLLGE 205
VAIVG GK++LI+++LGE
Sbjct: 646 VAIVGSTGEGKTSLISAMLGE 666
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme ethanolamine
ammonia lyase. The function of this gene is unknown,
although the presence of an N-terminal GxxGxGK motif
implies a GTP-binding site [Energy metabolism, Amino
acids and amines].
Length = 142
Score = 27.8 bits (62), Expect = 5.6
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 11/43 (25%)
Query: 184 KVAIVGKPNVGKSTLINSLLGE------NRVITY-----DTPG 215
++ +G GK+TL +L GE + + Y DTPG
Sbjct: 2 RIMFIGSVGCGKTTLTQALQGEEILYKKTQAVEYNDGAIDTPG 44
>gnl|CDD|198079 smart01011, AMP_N, Aminopeptidase P, N-terminal domain. This
domain is structurally very similar to the creatinase
N-terminal domain. However, little or no sequence
similarity exists between the two families.
Length = 135
Score = 28.0 bits (63), Expect = 5.7
Identities = 12/26 (46%), Positives = 13/26 (50%)
Query: 4 VLVLVGRPNVGKSTLFNRLTNSRDAL 29
VLVL GKSTLF + D L
Sbjct: 59 VLVLDPSGGGGKSTLFVPPRDPEDEL 84
>gnl|CDD|213265 cd03298, ABC_ThiQ_thiamine_transporter, ATP-binding cassette domain
of the thiamine transport system. Part of the
binding-protein-dependent transport system tbpA-thiPQ
for thiamine and TPP. Probably responsible for the
translocation of thiamine across the membrane. 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 = 211
Score = 28.2 bits (63), Expect = 5.9
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 6/37 (16%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDSI 221
AIVG GKSTL+N + G ++TP + R I
Sbjct: 27 TAIVGPSGSGKSTLLNLIAG------FETPQSGRVLI 57
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain only
a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 28.0 bits (63), Expect = 5.9
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 185 VAIVGKPNVGKSTLINSLLGENRVITYDT 213
+ +VG P GKST LL E + +
Sbjct: 2 ILMVGLPGSGKSTFARRLLRELGAVVLSS 30
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 28.9 bits (65), Expect = 6.0
Identities = 23/88 (26%), Positives = 36/88 (40%), Gaps = 18/88 (20%)
Query: 148 GNGIKNFLENILTIELPYKKFFKKKEFTNIHSIEYIK-----VAIVGKPNVGKSTLINSL 202
N + L KKF K F + ++ + ++G+P G STL+ ++
Sbjct: 51 PNALLKILTRGFRK---LKKFRDTKTFDILKPMDGLIKPGELTVVLGRPGSGCSTLLKTI 107
Query: 203 --------LGENRVITYDTPGTTRDSIK 222
+G VITYD G T + IK
Sbjct: 108 ASNTDGFHIGVEGVITYD--GITPEEIK 133
>gnl|CDD|183280 PRK11701, phnK, phosphonate C-P lyase system protein PhnK;
Provisional.
Length = 258
Score = 28.4 bits (64), Expect = 6.0
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 185 VAIVGKPNVGKSTLINSLLGE 205
+ IVG+ GK+TL+N+L
Sbjct: 35 LGIVGESGSGKTTLLNALSAR 55
>gnl|CDD|236729 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
Provisional.
Length = 638
Score = 29.0 bits (65), Expect = 6.1
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 184 KVAIVGKPNVGKSTLINSLLGE 205
KV +VGK GKSTL+ L E
Sbjct: 29 KVGLVGKNGCGKSTLLALLKNE 50
>gnl|CDD|188098 TIGR00957, MRP_assoc_pro, multi drug resistance-associated protein
(MRP). This model describes multi drug
resistance-associated protein (MRP) in eukaryotes. The
multidrug resistance-associated protein is an integral
membrane protein that causes multidrug resistance when
overexpressed in mammalian cells. It belongs to ABC
transporter superfamily. The protein topology and
function was experimentally demonstrated by epitope
tagging and immunofluorescence. Insertion of tags in the
critical regions associated with drug efflux, abrogated
its function. The C-terminal domain seem to highly
conserved [Transport and binding proteins, Other].
Length = 1522
Score = 29.1 bits (65), Expect = 6.3
Identities = 11/21 (52%), Positives = 17/21 (80%)
Query: 185 VAIVGKPNVGKSTLINSLLGE 205
VA+VG+ GKS+L+++LL E
Sbjct: 667 VAVVGQVGCGKSSLLSALLAE 687
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 28.7 bits (64), Expect = 6.3
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 15/61 (24%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGENRV---------------ITYDTPGTTRDSIKSLFEY 227
++V +VG VGKS+L++ ++ + + ITY +PG++ +SIK E
Sbjct: 22 VRVLVVGDSGVGKSSLVHLIVKGSSIARPPQTIGCTVGVKHITYGSPGSSSNSIKGDSER 81
Query: 228 N 228
+
Sbjct: 82 D 82
>gnl|CDD|224046 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component
[Inorganic ion transport and metabolism].
Length = 254
Score = 28.3 bits (64), Expect = 6.5
Identities = 11/21 (52%), Positives = 16/21 (76%), Gaps = 2/21 (9%)
Query: 185 VAIVGKPN-VGKSTLINSLLG 204
A++G PN GKSTL+ ++LG
Sbjct: 33 TALIG-PNGAGKSTLLKAILG 52
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 28.0 bits (63), Expect = 6.9
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 83 SDIIIFIVDGRQGLVEQDKLITNFLRKSGQPIVLVINK 120
D ++ +VD +GL + + + G P+VLVINK
Sbjct: 95 CDGVVLVVDVVEGLTSVTERLIRHAIQEGLPMVLVINK 132
>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
Provisional.
Length = 588
Score = 28.8 bits (65), Expect = 7.1
Identities = 13/18 (72%), Positives = 13/18 (72%)
Query: 185 VAIVGKPNVGKSTLINSL 202
VAIVG GKSTLIN L
Sbjct: 364 VAIVGPTGAGKSTLINLL 381
>gnl|CDD|224041 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 28.3 bits (64), Expect = 7.3
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 185 VAIVGKPNVGKSTLINSLLG 204
VAI+G GKSTL+ + G
Sbjct: 32 VAILGPSGCGKSTLLRLIAG 51
>gnl|CDD|223058 PHA03366, PHA03366, FGAM-synthase; Provisional.
Length = 1304
Score = 28.8 bits (65), Expect = 7.6
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 101 KLITNFLRKSGQPIVLV-INKSENINSSISLDFYELGIGNPHIISALYGNGIKNFLENIL 159
+T L+K G +V + I+ + S+ + L G IS Y +KN +
Sbjct: 805 PRLTPDLKKPGSALVHLSISPEYTLAGSVFEQIFGLKSGTLPDISPSY---LKNLFRAVQ 861
Query: 160 T 160
Sbjct: 862 H 862
>gnl|CDD|213220 cd03253, ABCC_ATM1_transporter, ATP-binding cassette domain of
iron-sulfur clusters transporter, subfamily C. ATM1 is
an ABC transporter that is expressed in the
mitochondria. Although the specific function of ATM1 is
unknown, its disruption results in the accumulation of
excess mitochondrial iron, loss of mitochondrial
cytochromes, oxidative damage to mitochondrial DNA, and
decreased levels of cytosolic heme proteins. 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 = 236
Score = 28.0 bits (63), Expect = 7.9
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 184 KVAIVGKPNVGKSTLINSLL 203
KVAIVG GKST++ L
Sbjct: 29 KVAIVGPSGSGKSTILRLLF 48
>gnl|CDD|227484 COG5155, ESP1, Separase, a protease involved in sister chromatid
separation [Cell division and chromosome partitioning /
Posttranslational modification, protein turnover,
chaperones].
Length = 1622
Score = 28.8 bits (64), Expect = 8.0
Identities = 20/123 (16%), Positives = 40/123 (32%), Gaps = 20/123 (16%)
Query: 246 TFEVIEKFSVIKTLKSILEA--NVVILLLDAQ-----QNISAQDINIANFIYESGRSLIV 298
E+ + K L +I+ N +L N+ ++ I+N S R+++
Sbjct: 412 LSEICIDYKEPKRLSNIISVLFNASVLFKSHSFLLKTANLEISNVLISNDSKTSHRTILK 471
Query: 299 CVNKWDSIIHNQRKI-------------IKNNIKKKLNFLSFAMFNFISAIKLNNINSFM 345
S Q+KI + + +F A + + +K+ F
Sbjct: 472 FEKFISSAQSAQKKIEIFSCLFNVYCMLRNDTLSFVFDFCQNAFIHCFTRLKITKFIEFS 531
Query: 346 ESI 348
S
Sbjct: 532 NSS 534
>gnl|CDD|239389 cd03115, SRP, The signal recognition particle (SRP) mediates the
transport to or across the plasma membrane in bacteria
and the endoplasmic reticulum in eukaryotes. SRP
recognizes N-terminal sighnal sequences of newly
synthesized polypeptides at the ribosome. The
SRP-polypeptide complex is then targeted to the membrane
by an interaction between SRP and its cognated receptor
(SR). In mammals, SRP consists of six protein subunits
and a 7SL RNA. One of these subunits is a 54 kd protein
(SRP54), which is a GTP-binding protein that interacts
with the signal sequence when it emerges from the
ribosome. SRP54 is a multidomain protein that consists
of an N-terminal domain, followed by a central G
(GTPase) domain and a C-terminal M domain.
Length = 173
Score = 27.9 bits (63), Expect = 8.0
Identities = 13/47 (27%), Positives = 29/47 (61%), Gaps = 5/47 (10%)
Query: 228 NNKKYILIDTAGIRRRNKTFEVIEKFSVIKTLKSILEANVVILLLDA 274
N +++DTAG R + ++E+ +K +K +++ + V+L++DA
Sbjct: 81 ENFDVVIVDTAG-RLQIDE-NLMEE---LKKIKRVVKPDEVLLVVDA 122
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible oxidation
of CO to CO2. CODH contains a nickel-iron-sulfur cluster
(C-center) and an iron-sulfur cluster (B-center). CO
oxidation occurs at the C-center. Three accessory
proteins encoded by cooCTJ genes are involved in nickel
incorporation into a nickel site. CooC functions as a
nickel insertase that mobilizes nickel to apoCODH using
energy released from ATP hydrolysis. CooC is a homodimer
and has NTPase activities. Mutation at the P-loop
abolishs its function.
Length = 116
Score = 27.2 bits (61), Expect = 8.0
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 184 KVAIVGKPNVGKSTL 198
K+AI GK VGK+T+
Sbjct: 1 KIAITGKGGVGKTTI 15
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family is
characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins), and
a characteristic second domain called COR (C-terminal of
Roc). A kinase domain and diverse regulatory domains are
also often found in Roco proteins. Their functions are
diverse; in Dictyostelium discoideum, which encodes 11
Roco proteins, they are involved in cell division,
chemotaxis and development, while in human, where 4 Roco
proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded,
these proteins are involved in epilepsy and cancer.
Mutations in LRRK2 (leucine-rich repeat kinase 2) are
known to cause familial Parkinson's disease.
Length = 161
Score = 27.7 bits (62), Expect = 8.3
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGENR 207
K+ +VG+ VGK++L L+GE
Sbjct: 2 AKLMLVGQGGVGKTSLCKQLIGEKF 26
>gnl|CDD|224677 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis
protein [Coenzyme metabolism].
Length = 161
Score = 27.7 bits (62), Expect = 8.3
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 185 VAIVGKPNVGKSTLINSLL 203
+ IVG N GK+TLI L+
Sbjct: 5 LGIVGYKNSGKTTLIEKLV 23
>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen
(La or SS-B or LARP3), La-related protein 7 (LARP7 or
PIP7S) and similar proteins. This subfamily corresponds
to the RRM2 of La and LARP7. La is a highly abundant
nuclear phosphoprotein and well conserved in eukaryotes.
It specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. LARP7
is an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3' -UUU-OH)
of 7SK RNA. It is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP), intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. LARP7 plays an essential role in the inhibition
of positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
Both La and LARP7 contain an N-terminal La motif (LAM),
followed by two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 26.1 bits (58), Expect = 8.4
Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 16/75 (21%)
Query: 209 ITYDTPGTTRDSIKSLF-EYNNKKYILI----DTAGIRRRNKTFEVIEKFSVIKTLKSIL 263
IT PG TR+ IK++F ++ KY+ DT IR F + +
Sbjct: 6 ITSIGPGVTREDIKAVFAQFGEVKYVDFTEGADTGYIR-----------FKTPEAAQKAR 54
Query: 264 EANVVILLLDAQQNI 278
EA V + I
Sbjct: 55 EAFVEKGEGLLGKEI 69
>gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast
Envelope Protein Translocase). [Transport and binding
proteins, Nucleosides, purines and pyrimidines].
Length = 313
Score = 28.3 bits (63), Expect = 8.7
Identities = 23/90 (25%), Positives = 45/90 (50%), Gaps = 14/90 (15%)
Query: 183 IKVAIVGKPNVGKSTLINSLLGEN--RVITYDTPG---TTRDSIKSLFEYNNKKYILIDT 237
+ + ++GK VGKS+ +NS++GE V + + G ++ F N +IDT
Sbjct: 39 LTILVMGKGGVGKSSTVNSIIGERIATVSAFQSEGLRPMMVSRTRAGFTLN-----IIDT 93
Query: 238 AGIRR----RNKTFEVIEKFSVIKTLKSIL 263
G+ ++ +I++F + KT+ +L
Sbjct: 94 PGLIEGGYINDQAVNIIKRFLLGKTIDVLL 123
>gnl|CDD|223998 COG1072, CoaA, Panthothenate kinase [Coenzyme metabolism].
Length = 283
Score = 28.0 bits (63), Expect = 8.9
Identities = 10/24 (41%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 175 TNIHSIEYIKVAIVGKPNVGKSTL 198
TN +I + I G VGKST
Sbjct: 76 TNNQQRPFI-IGIAGSVAVGKSTT 98
>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether
UreG binds GTP or some other nucleotide. Both enzymes
are involved in nickel binding. HypB can store nickel
and is required for nickel dependent hydrogenase
expression. UreG is required for functional
incorporation of the urease nickel metallocenter. GTP
hydrolysis may required by these proteins for nickel
incorporation into other nickel proteins. This family
of domains also contains P47K, a Pseudomonas
chlororaphis protein needed for nitrile hydratase
expression, and the cobW gene product, which may be
involved in cobalamin biosynthesis in Pseudomonas
denitrificans.
Length = 178
Score = 27.6 bits (62), Expect = 9.1
Identities = 10/26 (38%), Positives = 11/26 (42%)
Query: 3 PVLVLVGRPNVGKSTLFNRLTNSRDA 28
PV VL G GK+TL L
Sbjct: 1 PVTVLTGFLGSGKTTLLEHLLEKNRE 26
>gnl|CDD|192433 pfam09970, DUF2204, Nucleotidyl transferase of unknown function
(DUF2204). This domain, found in various hypothetical
archaeal proteins, has no known function. However, this
family was identified as belonging to the
nucleotidyltransferase superfamily.
Length = 181
Score = 27.7 bits (62), Expect = 9.7
Identities = 33/200 (16%), Positives = 69/200 (34%), Gaps = 28/200 (14%)
Query: 66 KGIMHEMTKQTKQAIIESDIIIFIVDGRQGLVEQ-DKLITNFLRKSGQPIVLVINKSENI 124
+ ++ ++ + ++ ++ + GR+G D I N +L + I
Sbjct: 6 GEVASKLQERGVKFVVIGGTVVPLALGRKGDTGDVDLFILNK------SPLLEEDFFREI 59
Query: 125 NSSISLDFYELGIGNPHIISALYGNGIK-NFLENILTIELPYKKFFKKKEFTNIHSIEYI 183
D+ +G P I+ + G ++ + ENIL +P + KE
Sbjct: 60 ADERGWDYGTTPLGTPRYIARVPGEEVRVDLYENILDFYVPEEILNDAKEV--------- 110
Query: 184 KVAIVGKPNVGKSTLINSLLGENRVITYDTPGTTRDS--IKSLFEYNNKKYILIDTAGIR 241
+G S+ E+ ++ + + Y + I ID I+
Sbjct: 111 --------AIGGVK-FKSIRLEDYIVLKARAAREEAEEFLDEIARYIPEGKISIDKRLIK 161
Query: 242 RRNKTFEVIEKFSVIKTLKS 261
+ F E S++K L+
Sbjct: 162 EHIELFPEEESESILKRLRE 181
>gnl|CDD|133306 cd04106, Rab23_like, Rab GTPase family 23 (Rab23)-like. Rab23-like
subfamily. Rab23 is a member of the Rab family of small
GTPases. In mouse, Rab23 has been shown to function as a
negative regulator in the sonic hedgehog (Shh) signaling
pathway. Rab23 mediates the activity of Gli2 and Gli3,
transcription factors that regulate Shh signaling in the
spinal cord, primarily by preventing Gli2 activation in
the absence of Shh ligand. Rab23 also regulates a step
in the cytoplasmic signal transduction pathway that
mediates the effect of Smoothened (one of two integral
membrane proteins that are essential components of the
Shh signaling pathway in vertebrates). In humans, Rab23
is expressed in the retina. Mice contain an isoform that
shares 93% sequence identity with the human Rab23 and an
alternative splicing isoform that is specific to the
brain. This isoform causes the murine open brain
phenotype, indicating it may have a role in the
development of the central nervous system. 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 facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. 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. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 162
Score = 27.4 bits (61), Expect = 10.0
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 183 IKVAIVGKPNVGKSTLI 199
IKV +VG NVGKS++I
Sbjct: 1 IKVIVVGNGNVGKSSMI 17
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
0.320 0.139 0.393
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,665,369
Number of extensions: 2187059
Number of successful extensions: 3547
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3355
Number of HSP's successfully gapped: 443
Length of query: 419
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 320
Effective length of database: 6,546,556
Effective search space: 2094897920
Effective search space used: 2094897920
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 (21.8 bits)
S2: 60 (26.8 bits)