RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780809|ref|YP_003065222.1| tRNA modification GTPase TrmE
[Candidatus Liberibacter asiaticus str. psy62]
(440 letters)
>gnl|CDD|179996 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 514 bits (1326), Expect = e-146
Identities = 184/450 (40%), Positives = 269/450 (59%), Gaps = 16/450 (3%)
Query: 4 EKETIFAVSTGALPSAISIIRLSGPSCFQVCEFICKKKKPFPRKASLRYFFGLDGRILDK 63
+TI A++T I IIR+SGP ++ + + KK P PR A + G ++D+
Sbjct: 3 MNDTIAAIATPPGRGGIGIIRISGPDALEIAQKLFGKKLPKPRTAHYGHIRD-PGEVIDE 61
Query: 64 GLLIVFPSPESFTGEDSAEFHVHGGIAVVNGILEELAKMPNLRLANPGEFSRRAFENGKI 123
L++ FP+P SFTGED E HGG AV+N ILE L + RLA PGEF++RAF NGK+
Sbjct: 62 VLVLYFPAPNSFTGEDVVEIQCHGGPAVLNLILELLLALG-ARLAEPGEFTKRAFLNGKL 120
Query: 124 DLLEAESLADLISSETEMQRRLSMEGMSGELSSLYGQWIDKLTHIRSFIEADLDFSEEED 183
DL +AE++ADLI ++TE RL++ + G LS L + ++L + + +EA +DF EE D
Sbjct: 121 DLTQAEAIADLIDAKTEAAARLALRQLQGALSKLINELREELLELLALVEAAIDFPEE-D 179
Query: 184 VQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKD 243
++ S +++L + L ++ + ++ + GEI+R G K+VI G N GKSSL NAL ++
Sbjct: 180 IEFLSDEKILEKLEELIAELEALLASARQGEILREGLKVVIAGRPNVGKSSLLNALLGEE 239
Query: 244 VAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVENADLIL 303
AIVTDI GTTRDV+ ++L+G +++ DTAGIRETDD VEK GI+R+ +E ADL+L
Sbjct: 240 RAIVTDIAGTTRDVIEEHINLDGIPLRLIDTAGIRETDDEVEKIGIERSREAIEEADLVL 299
Query: 304 LL------KEINSKKEISFPKNIDFIFIGTKSDLYSTYTEEYDH-----LISSFTGEGLE 352
L+ + + K+ I + K+DL E ++ IS+ TGEG++
Sbjct: 300 LVLDASEPLTEEDDEILEELKDKPVIVVLNKADLTGEIDLEEENGKPVIRISAKTGEGID 359
Query: 353 ELINKIKSILSNKFKKLPFS-IPSHKRHLYHLSQTVRYLEMASLN-EKDCGLDIIAENLR 410
EL IK + F ++ RHL L + + +LE A E L+++AE+LR
Sbjct: 360 ELREAIKELAFGGFGGNQEGVFLTNARHLEALERALEHLERALEGLESGLPLELLAEDLR 419
Query: 411 LASVSLGKITGCVDVEQLLDIIFSKFCIGK 440
LA +LG+ITG V E LLD IFS FCIGK
Sbjct: 420 LALEALGEITGEVTSEDLLDRIFSSFCIGK 449
>gnl|CDD|161885 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.
Length = 442
Score = 260 bits (667), Expect = 3e-70
Identities = 147/448 (32%), Positives = 232/448 (51%), Gaps = 25/448 (5%)
Query: 12 STGALPSAISIIRLSGPSCFQVCEFI-CKKKKPFPRKASLRYFFGLDGRILDKGLLIVFP 70
+T SAI IIRLSGP + + I K + + + + D LL F
Sbjct: 1 ATPPFNSAIHIIRLSGPDSLSILKKITNKLNTASGMRIQYGHIIDSNNKCKDDELLFKFV 60
Query: 71 SPESFTGEDSAEFHVHGGIAVVNGILEELAKMPNLRLANPGEFSRRAFENGKIDLLEAES 130
+P S+TGED E HG + +V IL+ K RLA PGEF++RAF NGK+DL +AE+
Sbjct: 61 APNSYTGEDVIEIQCHGSMLIVQEILQLCLKS-GARLAQPGEFTQRAFLNGKMDLTQAEA 119
Query: 131 LADLISSETEMQRRLSMEGMSGELSSLYGQWIDKLTHIRSFIEADLDFSEEEDVQNFSSK 190
+ +LI + + +++ ++GEL L + + +E ++D+ E++D Q+ ++
Sbjct: 120 INELILAPNNKVKDIALNKLAGELDQKIEAIRKSLLQLLAQVEVNIDYEEDDDEQDSLNQ 179
Query: 191 EVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDI 250
+L+ I LK+ I E + +G+K+ I+G N GKSSL NAL K+D AIV+DI
Sbjct: 180 LLLSIIAELKD-----ILNSYKLEKLDDGFKLAIVGSPNVGKSSLLNALLKQDRAIVSDI 234
Query: 251 PGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVENADLILLLKEINS 310
GTTRDV+ D +L G L+K+ DTAGIRE D VE+ GI+++F ++ ADL++ + + +
Sbjct: 235 KGTTRDVVEGDFELNGILIKLLDTAGIREHADFVERLGIEKSFKAIKQADLVIYVLDASQ 294
Query: 311 KKE-----ISFPK--NIDFIFIGTKSDLYSTYTEEYDHLISSFTG----------EGLEE 353
I FI + K DL E + + ++
Sbjct: 295 PLTKDDFLIIDLNKSKKPFILVLNKIDLKINSLEFFVSSKVLNSSNLSAKQLKIKALVDL 354
Query: 354 LINKIKSILSNKFKKLPFSIPSHKRHLYHLSQTVRYLE-MASLNEKDCGLDIIAENLRLA 412
L KI + S + +L + S + + L + + L+ S ++ LD++ +LR A
Sbjct: 355 LTQKINAFYSKERVELDDYLISSWQAMILLEKAIAQLQQFLSKLDRQLFLDMLVFHLREA 414
Query: 413 SVSLGKITGCVDVEQLLDIIFSKFCIGK 440
LG++TG V E +LD IFS FC+GK
Sbjct: 415 INCLGQVTGEVVTEDVLDEIFSNFCLGK 442
>gnl|CDD|150979 pfam10396, TrmE_N, GTP-binding protein TrmE N-terminus. This
family represents the shorter, B, chain of the
homo-dimeric structure which is a guanine
nucleotide-binding protein that binds and hydrolyses
GTP. TrmE is homologous to the tetrahydrofolate-binding
domain of N,N-dimethylglycine oxidase and indeed binds
formyl-tetrahydrofolate. TrmE actively participates in
the formylation reaction of uridine and regulates the
ensuing hydrogenation reaction of a Schiff's base
intermediate. This B chain is the N-terminal portion of
the protein consisting of five beta-strands and three
alpha helices and is necessary for mediating dimer
formation within the protein.
Length = 114
Score = 168 bits (428), Expect = 3e-42
Identities = 54/116 (46%), Positives = 72/116 (62%), Gaps = 2/116 (1%)
Query: 7 TIFAVSTGALPSAISIIRLSGPSCFQVCEFICKKKKPFPRKASLRYFFGLDGRILDKGLL 66
TI A++T I+IIR+SGP ++ + + K P PR A +G ++D+ L+
Sbjct: 1 TIAAIATPPGRGGIAIIRISGPDALEIAKKLFGKL-PKPRTAHYGTIRDPNGEVIDEVLV 59
Query: 67 IVFPSPESFTGEDSAEFHVHGGIAVVNGILEELAKMPNLRLANPGEFSRRAFENGK 122
+ FP+P SFTGED E H HGG AVV IL+ L K+ RLA PGEF+RRAF NGK
Sbjct: 60 LYFPAPNSFTGEDVVEIHCHGGPAVVQAILQALLKLG-ARLAEPGEFTRRAFLNGK 114
>gnl|CDD|163343 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.
Length = 429
Score = 97.9 bits (245), Expect = 4e-21
Identities = 52/180 (28%), Positives = 87/180 (48%), Gaps = 32/180 (17%)
Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR-- 278
KI I+G N GKS+L NAL ++ IV+DI GTTRD + I + G + DTAGIR
Sbjct: 174 KIAIIGRPNVGKSTLVNALLGEERVIVSDIAGTTRDSIDIPFERNGKKYLLIDTAGIRRK 233
Query: 279 -ETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEIS----------FPKNIDFIFIGT 327
+ + VEK + RT +E AD++LL+ +++ + I+ + +
Sbjct: 234 GKVTEGVEKYSVLRTLKAIERADVVLLV--LDATEGITEQDLRIAGLILEAGKALVIVVN 291
Query: 328 KSDL------YSTYTEEYD-----------HLISSFTGEGLEELINKIKSILSNKFKKLP 370
K DL + +E IS+ TG+G+++L++ I + N +++
Sbjct: 292 KWDLVKDEKTREEFKKELRRKLPFLDFAPIVFISALTGQGVDKLLDAIDEVYENANRRIS 351
Score = 81.3 bits (202), Expect = 5e-16
Identities = 45/164 (27%), Positives = 75/164 (45%), Gaps = 21/164 (12%)
Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRET 280
+ I+G N GKS+LFN L K AIV+D PG TRD D + G + DT GI E
Sbjct: 1 VVAIVGRPNVGKSTLFNRLTGKRDAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGIEED 60
Query: 281 DDIVEKEGIKRTFLEVENADLILLLKEINSKKEIS----------FPKNIDFIFIGTKSD 330
DD ++K+ ++ + +E AD+IL + ++ ++ ++ I + K D
Sbjct: 61 DDGLDKQIREQAEIAIEEADVILFV--VDGREGLTPEDEEIAKWLRKSGKPVILVANKID 118
Query: 331 LYSTYTEEYD---------HLISSFTGEGLEELINKIKSILSNK 365
+ IS+ G G+ +L++ I +L +
Sbjct: 119 GKKEDAVAAEFYSLGFGEPIPISAEHGRGIGDLLDAILELLPEE 162
>gnl|CDD|178858 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 94.4 bits (236), Expect = 5e-20
Identities = 56/179 (31%), Positives = 87/179 (48%), Gaps = 31/179 (17%)
Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR-- 278
KI I+G N GKSSL NAL ++ IV+DI GTTRD + + +G + DTAGIR
Sbjct: 175 KIAIIGRPNVGKSSLINALLGEERVIVSDIAGTTRDSIDTPFERDGQKYTLIDTAGIRRK 234
Query: 279 -ETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEIS-FPKNI-DF--------IFIGT 327
+ + VEK + RT +E AD++LL+ I++ + I+ I + +
Sbjct: 235 GKVTEGVEKYSVIRTLKAIERADVVLLV--IDATEGITEQDLRIAGLALEAGRALVIVVN 292
Query: 328 KSDLYSTYT-EEYD---------------HLISSFTGEGLEELINKIKSILSNKFKKLP 370
K DL T EE+ IS+ TG+G+++L+ I N +++
Sbjct: 293 KWDLVDEKTMEEFKKELRRRLPFLDYAPIVFISALTGQGVDKLLEAIDEAYENANRRIS 351
Score = 83.2 bits (207), Expect = 1e-16
Identities = 47/162 (29%), Positives = 76/162 (46%), Gaps = 23/162 (14%)
Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRET 280
+ I+G N GKS+LFN L K AIV D PG TRD + + + G + DT GI
Sbjct: 3 VVAIVGRPNVGKSTLFNRLTGKRDAIVADTPGVTRDRIYGEAEWLGREFILIDTGGIEPD 62
Query: 281 DDIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDF-----------IFIGTKS 329
DD EK+ ++ L +E AD+IL + ++ + ++ P + + I + K
Sbjct: 63 DDGFEKQIREQAELAIEEADVILFV--VDGRAGLT-PADEEIAKILRKSNKPVILVVNKV 119
Query: 330 DLYSTYTEEYD---------HLISSFTGEGLEELINKIKSIL 362
D + Y+ + IS+ G G+ +L++ I L
Sbjct: 120 DGPDEEADAYEFYSLGLGEPYPISAEHGRGIGDLLDAILEEL 161
>gnl|CDD|161778 TIGR00231, small_GTP, small GTP-binding protein domain. 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.
Length = 161
Score = 63.2 bits (154), Expect = 1e-10
Identities = 38/121 (31%), Positives = 58/121 (47%), Gaps = 11/121 (9%)
Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLT--IDLDLEGYLVKISDTAGI 277
KIVI+G N GKS+L N L I PGTTR+ +T I+ D + Y + DTAG
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNK-FITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG- 59
Query: 278 RETDDIVEKEGIKRTFLEVENADLILLLKEINS-----KKEI--SFPKNIDFIFIGTKSD 330
+E + + + + D+++L+ ++ KEI N+ I +G K D
Sbjct: 60 QEDYRAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESNVPIILVGNKID 119
Query: 331 L 331
L
Sbjct: 120 L 120
>gnl|CDD|161878 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.
Length = 591
Score = 55.9 bits (135), Expect = 2e-08
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 226 GHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVE 285
G+ N GKS+LFNAL + V + PG T + L +G ++I D GI
Sbjct: 1 GNPNVGKSTLFNALTGAN-QTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFSL 59
Query: 286 KEGIKRTFLEVENADLIL 303
+E + R +L E DL++
Sbjct: 60 EEEVARDYLLNEKPDLVV 77
>gnl|CDD|178854 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 54.7 bits (133), Expect = 5e-08
Identities = 38/165 (23%), Positives = 71/165 (43%), Gaps = 26/165 (15%)
Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETD 281
+ I+G N GKS+L NAL + ++IV+ P TTR + + + + DT GI +
Sbjct: 8 VAIVGRPNVGKSTLLNALVGQKISIVSPKPQTTRHRIRGIVTEDDAQIIFVDTPGIHKPK 67
Query: 282 DIVEKEGIKRTFLEVENADLILLLKEINSKKEISF----------PKNIDFIFIGTKSDL 331
+ + K + +++ DL+L + +++ ++I I + K DL
Sbjct: 68 RALNRAMNKAAWSSLKDVDLVLFV--VDADEKIGPGDEFILEKLKKVKTPVILVLNKIDL 125
Query: 332 ----------YSTYTEEYDHL----ISSFTGEGLEELINKIKSIL 362
+E D IS+ G+ ++EL++ I L
Sbjct: 126 VKDKEELLPLLEELSELMDFAEIVPISALKGDNVDELLDVIAKYL 170
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 54.6 bits (132), Expect = 6e-08
Identities = 23/58 (39%), Positives = 37/58 (63%)
Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR 278
++ ++G N GKSSL N LA ++ ++V D+ GTT D + ++L G + DTAG+R
Sbjct: 213 RVALVGKPNVGKSSLLNKLAGEERSVVDDVAGTTVDPVDSLIELGGKTWRFVDTAGLR 270
Score = 42.6 bits (101), Expect = 2e-04
Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 10/86 (11%)
Query: 224 ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDI 283
++G N GKS+L N + + A+V D+PG TRD ++ D + G + DT G E D
Sbjct: 43 VVGRPNVGKSTLVNRILGRREAVVEDVPGVTRDRVSYDAEWNGRRFTVVDTGGW-EPD-- 99
Query: 284 VEKEGIKRTFLE-----VENADLILL 304
+G++ + E + AD +L
Sbjct: 100 --AKGLQASVAEQAEVAMRTADAVLF 123
>gnl|CDD|163162 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).
Length = 351
Score = 54.4 bits (132), Expect = 6e-08
Identities = 54/176 (30%), Positives = 77/176 (43%), Gaps = 40/176 (22%)
Query: 217 RNGYKIVIL-GHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDL-EGYLVKISDT 274
R V L G++NAGKS+LFNAL DV D T D T LDL +G V ++DT
Sbjct: 186 RADVPTVALVGYTNAGKSTLFNALTGADV-YAADQLFATLDPTTRRLDLPDGGEVLLTDT 244
Query: 275 AG-IRE-TDDIVEKEGIKRTFLEVENADLIL-------------------LLKEINSKKE 313
G IR+ ++V + T EV ADL+L +L+E+ +
Sbjct: 245 VGFIRDLPHELV--AAFRATLEEVREADLLLHVVDASDPDREEQIEAVEKVLEELGA--- 299
Query: 314 ISFPKNIDFIFIGTKSDLYSTYTEEYDH-------LISSFTGEGLEELINKIKSIL 362
++I + + K DL E +S+ TGEGL+ L+ I L
Sbjct: 300 ----EDIPQLLVYNKIDLLDEPRIERLEEGYPEAVFVSAKTGEGLDLLLEAIAERL 351
>gnl|CDD|181925 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 52.5 bits (126), Expect = 2e-07
Identities = 23/58 (39%), Positives = 37/58 (63%)
Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR 278
++ ++G N GKSSL N L ++ A+V D+ GTTRD + ++++G DTAGI+
Sbjct: 452 RVALVGRPNVGKSSLLNQLTHEERAVVNDLAGTTRDPVDEIVEIDGEDWLFIDTAGIK 509
Score = 49.4 bits (118), Expect = 2e-06
Identities = 50/238 (21%), Positives = 90/238 (37%), Gaps = 33/238 (13%)
Query: 174 ADLDFSE---------EEDVQNF-SSKEVLNDILFLKNDISSHI------SQGKLGEIIR 217
+DLDF E E+ ++ + N + ++ + G +
Sbjct: 214 SDLDFDETLDLLIGLVEDAIEEQEYDQYAANLEGYELDEGDEDLLEGSGFVAGDEKAGPK 273
Query: 218 NGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGI 277
+ I+G N GKS+L N + + A+V D PG TRD ++ D + G K+ DT G
Sbjct: 274 AVGVVAIVGRPNVGKSTLVNRILGRREAVVEDTPGVTRDRVSYDAEWAGTDFKLVDTGGW 333
Query: 278 RETDDIVEKEGIKRTFLEVENADLILLLKE----INSKKEISFPK----NIDFIFIGTKS 329
+ ++ + + V AD ++ + + + S E + K
Sbjct: 334 EADVEGIDSAIASQAQIAVSLADAVVFVVDGQVGLTSTDERIVRMLRRAGKPVVLAVNKI 393
Query: 330 DLYSTY--TEEYDHL-------ISSFTGEGLEELINKIKSILSNKFKKLPFSIPSHKR 378
D ++ E+ L IS+ G G+ +L+++ L K F PS R
Sbjct: 394 DDQASEYDAAEFWKLGLGEPYPISAMHGRGVGDLLDEALDSLKVAEKTSGFLTPSGLR 451
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 52.0 bits (124), Expect = 3e-07
Identities = 49/159 (30%), Positives = 82/159 (51%), Gaps = 20/159 (12%)
Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETD 281
+ I+G N+GKS+L N + + ++IVT TTR ++T + L+ V + DT GI E
Sbjct: 55 VCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPGIFEPK 114
Query: 282 DIVEKEGIKRTFLEVENADLILL-LKEINSKKEISF-------PKNIDFIFIGTKSDLYS 333
+EK ++ + + +ADL+LL + + S +I+ NI IF+ K D+ S
Sbjct: 115 GSLEKAMVRCAWSSLHSADLVLLIIDSLKSFDDITHNILDKLRSLNIVPIFLLNKIDIES 174
Query: 334 TY--------TEEY-DHL---ISSFTGEGLEELINKIKS 360
Y TE + D L IS+ +G+ ++ L+ I S
Sbjct: 175 KYLNDIKAFLTENHPDSLLFPISALSGKNIDGLLEYITS 213
>gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 51.4 bits (124), Expect = 5e-07
Identities = 26/81 (32%), Positives = 33/81 (40%), Gaps = 11/81 (13%)
Query: 223 VILGHSNAGKSSLFNALAKKDVAIVTDIPG-------TTRDVLTIDLDLEGYLVKISDTA 275
V+ G S GKS+L NALA +I TT V DL G L+ DT
Sbjct: 168 VLAGQSGVGKSTLLNALAPDLELKTGEISEALGRGKHTTTHVELYDLPGGGLLI---DTP 224
Query: 276 GIRETD-DIVEKEGIKRTFLE 295
G +E E ++ F E
Sbjct: 225 GFSSFGLHDLEAEELEHYFPE 245
>gnl|CDD|132636 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.
Length = 360
Score = 50.7 bits (122), Expect = 7e-07
Identities = 36/111 (32%), Positives = 48/111 (43%), Gaps = 29/111 (26%)
Query: 214 EIIRNGYKIVILGHSNAGKSSLFNALAK-----KDVAIVTDIPGTTRDVLTIDLDLEGYL 268
+ RN + ++G +N GKSSL N L K KDV + PGTT D++ I LD L
Sbjct: 149 KKARNKKDVYVVGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLDDGHSL 208
Query: 269 VKISDTAGI----RETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEIS 315
DT GI + + +K+ LK I KKEI
Sbjct: 209 Y---DTPGIINSHQMAHYLDKKD-----------------LKYITPKKEIK 239
>gnl|CDD|163345 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.
Length = 276
Score = 44.8 bits (107), Expect = 5e-05
Identities = 23/57 (40%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGI 277
+ +I+G N GKS+L N LA K VA V + PG T+ I L +++ DT GI
Sbjct: 120 RAMIVGIPNVGKSTLINRLAGKKVAKVGNRPGVTKGQQWIKLSDG---LELLDTPGI 173
>gnl|CDD|179346 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 43.0 bits (102), Expect = 2e-04
Identities = 30/109 (27%), Positives = 50/109 (45%), Gaps = 22/109 (20%)
Query: 203 ISSHISQG--KLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPG-------- 252
+S+ +G L + G + +LG S GKS+L NAL ++V +
Sbjct: 177 VSALDGEGLDVLAAWLSGGKTVALLGSSGVGKSTLVNALLGEEVQKTGAVREDDSKGRHT 236
Query: 253 -TTRDVLTIDLDLEGYLVKISDTAGIRE---TDDIVEKEGIKRTFLEVE 297
T R++ L G L+ DT G+RE D ++G++ TF ++E
Sbjct: 237 TTHRELHP--LPSGGLLI---DTPGMRELQLWD---AEDGVEETFSDIE 277
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 43.0 bits (102), Expect = 2e-04
Identities = 30/92 (32%), Positives = 42/92 (45%), Gaps = 17/92 (18%)
Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTR--------DVLTIDLDLEGYLVKIS 272
+IV +G SN GKS+L L K V V PG TR D + DL G++ +
Sbjct: 11 EIVFVGRSNVGKSTLVRELTGKKVR-VGKRPGVTRKPNHYDWGDFILTDLPGFGFMSGVP 69
Query: 273 DTAGIRETDDIVEKEGIKRTFLEVENADLILL 304
+ D+IV ++E +NAD IL
Sbjct: 70 KEVQEKIKDEIVR-------YIE-DNADRILA 93
>gnl|CDD|184332 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 42.9 bits (102), Expect = 2e-04
Identities = 36/107 (33%), Positives = 49/107 (45%), Gaps = 29/107 (27%)
Query: 217 RNGYKIVILGHSNAGKSSLFNALAK-----KDVAIVTDIPGTTRDVLTIDLDLEGYLVKI 271
R G + ++G +N GKS+L N + K KDV + PGTT D + I LD +L
Sbjct: 158 REGRDVYVVGVTNVGKSTLINRIIKEITGEKDVITTSRFPGTTLDKIEIPLDDGSFLY-- 215
Query: 272 SDTAGIRETDDIVEKEGIKR----TFLEVENADLILLLKEINSKKEI 314
DT GI I R +L ++ LK I+ KKEI
Sbjct: 216 -DTPGI-----------IHRHQMAHYLSAKD------LKIISPKKEI 244
>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.
Length = 270
Score = 42.0 bits (99), Expect = 3e-04
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD-VLTIDLDLEGYLVKISDTAGIRE 279
+ ILG N GKS+L N L + ++I + TTR+ + I ++ I DT G E
Sbjct: 2 FVAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFI-DTPGFHE 60
>gnl|CDD|181957 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 41.7 bits (99), Expect = 4e-04
Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGI 277
+ +I+G N GKS+L N LA K +A + PG T+ I L +++ DT GI
Sbjct: 123 RAMIIGIPNVGKSTLINRLAGKKIAKTGNRPGVTKAQQWIKLGKG---LELLDTPGI 176
>gnl|CDD|161735 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
The Aquifex aeolicus ortholog is split into consecutive
open reading frames. Consequently, this model was build
in fragment mode (-f option).
Length = 245
Score = 41.2 bits (97), Expect = 6e-04
Identities = 36/135 (26%), Positives = 51/135 (37%), Gaps = 22/135 (16%)
Query: 177 DFSEEEDVQNFSSKEVLN---DILFLKNDISSHISQG--KLGEIIRNGYKIVILGHSNAG 231
D ++ED++ N +L SS G +L E ++N + G S G
Sbjct: 78 DLLDDEDMEKEQLDIYRNIGYQVLM----TSSKNQDGLKELIEALQNRISVFA-GQSGVG 132
Query: 232 KSSLFNALAKKDVAIVTDIPG-------TTRDVLTIDLDLEGYLVKISDTAGIRETD-DI 283
KSSL NAL V DI TT V G + DT G E
Sbjct: 133 KSSLINALDPSVKQQVNDISSKLGLGKHTTTHVELFHFH-GGLIA---DTPGFNEFGLWH 188
Query: 284 VEKEGIKRTFLEVEN 298
+E E + + F+E +
Sbjct: 189 LEPEQLTQGFVEFRD 203
>gnl|CDD|179035 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 40.5 bits (96), Expect = 0.001
Identities = 44/183 (24%), Positives = 74/183 (40%), Gaps = 44/183 (24%)
Query: 218 NGYKIVILGHSNAGKSSLFNALA-KKDVAIVTDIPGTTRDVLTI---DLDLEGYLV---- 269
+G +I G SN GKSSL NAL +K++A + PG T+ I +++ + LV
Sbjct: 23 DGPEIAFAGRSNVGKSSLINALTNRKNLARTSKTPGRTQ---LINFFEVNDKLRLVDLPG 79
Query: 270 ----KISDTAGIRE------TDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISF--P 317
K+S +E + + +E +K L + D LKE++ + I +
Sbjct: 80 YGYAKVSKE--EKEKWQKLIEEYLRTRENLKGVVLLI---DSRHPLKELD-LQMIEWLKE 133
Query: 318 KNIDFIFIGTKSD---------LYSTYTEEYD------HLISSFTGEGLEELINKIKSIL 362
I + + TK+D + L SS +G++EL I L
Sbjct: 134 YGIPVLIVLTKADKLKKGERKKQLKKVRKALKFGDDEVILFSSLKKQGIDELRAAIAKWL 193
Query: 363 SNK 365
+
Sbjct: 194 AEA 196
>gnl|CDD|149505 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 = 118
Score = 39.3 bits (92), Expect = 0.002
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 28/128 (21%)
Query: 221 KIVILGHSNAGKSSLFNALAK--KDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR 278
K+V++G +GKSSL + L I +I G T V T+++D + L+ I D G R
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEIPEEIQGDTLAVDTLEVDGDTELLHIWDFGG-R 59
Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISF----------------PKNIDF 322
E E + ++ AD ILL+ + S K I
Sbjct: 60 E-------ELKFEHIIFMKTADAILLV--YDLTDRESLNRVSRLIAWLPHLRKLGKKIPV 110
Query: 323 IFIGTKSD 330
I +G K D
Sbjct: 111 ILVGNKFD 118
>gnl|CDD|128472 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 37.5 bits (88), Expect = 0.007
Identities = 34/131 (25%), Positives = 51/131 (38%), Gaps = 33/131 (25%)
Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVK--ISDTAG- 276
+KI+++G S GKSSL + D T ++++G VK I DTAG
Sbjct: 1 FKIILIGDSGVGKSSLLSRFT-DGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQ 59
Query: 277 ----------IRETD------DIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNI 320
R DI +E +F ++N LKE+ N+
Sbjct: 60 ERFRSITSSYYRGAVGALLVYDITNRE----SFENLKN-----WLKELREYA----DPNV 106
Query: 321 DFIFIGTKSDL 331
+ +G KSDL
Sbjct: 107 VIMLVGNKSDL 117
>gnl|CDD|163346 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.
Length = 179
Score = 37.1 bits (87), Expect = 0.008
Identities = 18/39 (46%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 218 NGYKIVILGHSNAGKSSLFNALAK-KDVAIVTDIPGTTR 255
+G +I G SN GKSSL NAL K +A + PG T+
Sbjct: 17 DGPEIAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQ 55
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 36.2 bits (84), Expect = 0.016
Identities = 29/85 (34%), Positives = 43/85 (50%), Gaps = 6/85 (7%)
Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVL-TIDLDLEGYLVKISDTAG-IRE 279
+ ++G++NAGKS+LFN + + V + T L ID+ G V ++DT G IR
Sbjct: 200 VSLVGYTNAGKSTLFNRITEARVYAADQLFATLDPTLRRIDVADVGETV-LADTVGFIRH 258
Query: 280 -TDDIVEKEGIKRTFLEVENADLIL 303
D+V K T E A L+L
Sbjct: 259 LPHDLV--AAFKATLQETRQATLLL 281
>gnl|CDD|183014 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 36.0 bits (84), Expect = 0.018
Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 11/78 (14%)
Query: 168 IRSFIEADLDFSEEEDVQNFSSKEVLNDILFLKN-DISSHISQGK--LGEI---IRNGYK 221
+ +F+E L ++ + + +S + + + ++ +I S GK G + + G +
Sbjct: 324 LVTFLETPLAHPQQGE-KELASNDPVT--IEAEDLEILSP--DGKTLAGPLNFTLPAGQR 378
Query: 222 IVILGHSNAGKSSLFNAL 239
I ++G S AGK+SL NAL
Sbjct: 379 IALVGPSGAGKTSLLNAL 396
>gnl|CDD|181982 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 34.4 bits (80), Expect = 0.055
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD 256
I ++G N GKS+ FNA DV I + P TT D
Sbjct: 2 ITIGLVGKPNVGKSTFFNAATLADVEI-ANYPFTTID 37
>gnl|CDD|178387 PLN02790, PLN02790, transketolase.
Length = 654
Score = 34.6 bits (80), Expect = 0.056
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 9/45 (20%)
Query: 147 MEGMSGELSSLYGQW-IDKLT------HIRSFIEADLDFSEEEDV 184
MEG+S E +SL G W + KL HI I+ D + + EDV
Sbjct: 150 MEGISNEAASLAGHWGLGKLIVLYDDNHIS--IDGDTEIAFTEDV 192
>gnl|CDD|181981 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 33.5 bits (78), Expect = 0.10
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 219 GYKIVILGHSNAGKSSLFNALAKKDVAI 246
G K I+G N GKS+LFNAL K
Sbjct: 2 GLKCGIVGLPNVGKSTLFNALTKAGAEA 29
>gnl|CDD|163042 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit.
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 = 33.4 bits (77), Expect = 0.12
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
+ G ++ ++G S AGKS+L N L
Sbjct: 345 VPPGERVALVGPSGAGKSTLLNLLL 369
>gnl|CDD|162989 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.
Length = 329
Score = 32.4 bits (75), Expect = 0.24
Identities = 44/208 (21%), Positives = 80/208 (38%), Gaps = 74/208 (35%)
Query: 210 GKLGEI--IRNGYKIV----ILGHSNAGKSSLFNAL--AKKDVA---------------- 245
G+ GE +R K++ ++G NAGKS+L +A+ AK +A
Sbjct: 142 GEPGEERWLRLELKLLADVGLVGLPNAGKSTLISAVSAAKPKIADYPFTTLVPNLGVVRV 201
Query: 246 ------IVTDIPGTTRDVLTIDLDLEG-------------------YLVKISDTAGIRET 280
++ DIPG +EG L+ + D + + +
Sbjct: 202 DDGRSFVIADIPGL----------IEGASEGAGLGHRFLKHIERTRVLLHLIDISPL-DG 250
Query: 281 DDIVEKEGIKRTFLEVENADL-----ILLLKEINSKKEISFPKNIDFIFIGTKSDLYSTY 335
D +E I R L+ + +L I++L +I+ E + + + ++
Sbjct: 251 RDPIEDYEIIRNELKKYSPELAEKPRIVVLNKIDLLDEEELAELLKELKKALGKPVF--- 307
Query: 336 TEEYDHLISSFTGEGLEELINKIKSILS 363
IS+ TGEGL+EL+ + +L
Sbjct: 308 ------PISALTGEGLDELLYALAELLE 329
>gnl|CDD|162130 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP)
Family protein.
Length = 617
Score = 32.3 bits (74), Expect = 0.24
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 9/42 (21%)
Query: 199 LKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALA 240
L ++S G+L + ++G S AGK++L NALA
Sbjct: 40 LLKNVSGVAKPGEL---------LAVMGSSGAGKTTLMNALA 72
>gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit;
Provisional.
Length = 232
Score = 32.2 bits (74), Expect = 0.25
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
+ G ++ ILG S AGKS+L N +A
Sbjct: 22 VERGERVAILGPSGAGKSTLLNLIA 46
>gnl|CDD|185530 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 31.5 bits (72), Expect = 0.42
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 218 NGYKIVILGHSNAGKSSLFNALAKKDV 244
N K+ I+G N GKS+ FNAL K+ V
Sbjct: 20 NNLKMGIVGLPNVGKSTTFNALCKQQV 46
>gnl|CDD|183417 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 30.8 bits (71), Expect = 0.67
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 342 LISSFTGEGLEELINKIKSILS 363
LIS+ TGEGL+EL+ + +L
Sbjct: 307 LISAVTGEGLDELLRALWELLE 328
Score = 27.7 bits (63), Expect = 6.0
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 5/33 (15%)
Query: 224 ILGHSNAGKSSLFNAL--AKKDVAIVTDIPGTT 254
++G NAGKS+L +A+ AK +A D P TT
Sbjct: 163 LVGLPNAGKSTLISAVSAAKPKIA---DYPFTT 192
>gnl|CDD|178676 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 30.5 bits (69), Expect = 0.80
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 216 IRNGYKIVILGHSNAGKSSLFNAL 239
I K+ I+G + AGKSS+ NAL
Sbjct: 1262 ISPSEKVGIVGRTGAGKSSMLNAL 1285
>gnl|CDD|173562 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 30.2 bits (68), Expect = 0.96
Identities = 42/144 (29%), Positives = 60/144 (41%), Gaps = 21/144 (14%)
Query: 218 NGYKIVILGHSNAGKSSLFNALAKKDVAIVTD--IPGTTRDVLTIDLDLEGYLVKISDTA 275
YK+V++G GKS+L + D I + R ID + L+ I DTA
Sbjct: 4 TEYKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEET--CLLDILDTA 61
Query: 276 GIRETDDIVEKEGIKRT---FLEVENADLILLLKEINS-KKEISFPKNID---FIFIGTK 328
G E + ++ RT FL V + +EI S +++I K+ D I +G K
Sbjct: 62 GQEEYSAM--RDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNK 119
Query: 329 SDLYSTYTEEYDHLISSFTGEGLE 352
DL D TGEG E
Sbjct: 120 CDL--------DSERQVSTGEGQE 135
>gnl|CDD|130252 TIGR01184, ntrCD, nitrate transport ATP-binding subunits C and D.
This model describes the ATP binding subunits of nitrate
transport in bacteria and archaea. This protein belongs
to the ATP-binding cassette (ABC) superfamily. It is
thought that the two subunits encoded by ntrC and ntrD
form the binding surface for interaction with ATP. This
model is restricted in identifying ATP binding subunit
associated with the nitrate transport. Nitrate
assimilation is aided by other proteins derived from the
operon which among others include products of ntrA - a
regulatory protein; ntrB - a hydropbobic transmembrane
permease and narB - a reductase.
Length = 230
Score = 29.7 bits (67), Expect = 1.4
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
I+ G I ++GHS GKS+L N ++
Sbjct: 8 IQQGEFISLIGHSGCGKSTLLNLIS 32
>gnl|CDD|161805 TIGR00287, cas1, CRISPR-associated endonuclease Cas1. This model
identifies CRISPR-associated protein Cas1, the most
universal CRISPR system protein. CRISPR is an acronym
for Clustered Regularly Interspaced Short Palindromic
Repeats, a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA.
Cas1 is a metal-dependent DNA-specific endonuclease.
Length = 323
Score = 29.6 bits (67), Expect = 1.6
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 283 IVEKEGIKRTFLEVENADLILLLKEIN-SKKEISF--PKNIDFIFIGTKSD-LYSTYTEE 338
+VEKEG K+ + V N D I+L ++ S I + ID +F+G + L +E
Sbjct: 19 VVEKEGKKKWNIPVANVDCIVLFGGVSISSAAIRELAKRGIDIVFLGGDGNYLGRLSPQE 78
Query: 339 YDH 341
Sbjct: 79 SGS 81
>gnl|CDD|180911 PRK07261, PRK07261, topology modulation protein; Provisional.
Length = 171
Score = 29.7 bits (67), Expect = 1.7
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 221 KIVILGHSNAGKSSLFNALAKK 242
KI I+G+S +GKS+L L++
Sbjct: 2 KIAIIGYSGSGKSTLARKLSQH 23
>gnl|CDD|168499 PRK06274, PRK06274, indolepyruvate oxidoreductase subunit B;
Reviewed.
Length = 197
Score = 29.2 bits (66), Expect = 2.0
Identities = 24/112 (21%), Positives = 47/112 (41%), Gaps = 13/112 (11%)
Query: 265 EGYLVKISDTAGIRETDDIVEK-----EGIKRTFLEVENADLILLLKEINSKKEISFPKN 319
EG+ V+ ++T G+ + + V + I + ADL+L L+ + + F K
Sbjct: 29 EGFHVRTAETLGMSQREGSVISHLRFGDEISSPLIPEGQADLLLALEPAEVARNLHFLKK 88
Query: 320 IDFIFIGTKSDLYST--YTEEYDHLISSFTGEGLEELINKIKSILSNKFKKL 369
I + + +T +E+YD + ++ KI ++ F KL
Sbjct: 89 GGKIIVNAYAIHPATTVGSEKYDPE------KEIKFAKEKICDVICIDFTKL 134
>gnl|CDD|128471 smart00174, RHO, Rho (Ras homology) subfamily of Ras-like small
GTPases. Members of this subfamily of Ras-like small
GTPases include Cdc42 and Rac, as well as Rho isoforms.
Length = 174
Score = 29.5 bits (67), Expect = 2.0
Identities = 40/158 (25%), Positives = 67/158 (42%), Gaps = 29/158 (18%)
Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTD-IPGTTRDVLTIDLDLEGYLVKIS--DTAGIR 278
+V++G GK+ L + A D +P T + + D++++G V++ DTAG
Sbjct: 1 LVVVGDGAVGKTCLLISYTTN--AFPEDYVP-TVFENYSADVEVDGKPVELGLWDTAGQE 57
Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINS--------KK---EIS-FPKNIDFIFIG 326
+ D + R L + D+ L+ ++S +K E+ F N I +G
Sbjct: 58 DYDRL-------RP-LSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFCPNTPIILVG 109
Query: 327 TKSDLY---STYTEEYDHLISSFTGEGLEELINKIKSI 361
TK DL ST E T E E L +I ++
Sbjct: 110 TKLDLREDKSTLRELSKQKQEPVTYEQGEALAKRIGAV 147
>gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein.
Length = 1394
Score = 29.3 bits (66), Expect = 2.1
Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 10/82 (12%)
Query: 178 FSEEEDVQN--FSSKEVLNDILFLKN-DISSHISQGK---LGEI---IRNGYKIVILGHS 228
E +DV + KE DI +N I + K L + ++ G ++G S
Sbjct: 739 TDESDDVNDEKDMEKESGEDIFHWRNLTYEVKIKKEKRVILNNVDGWVKPGTLTALMGAS 798
Query: 229 NAGKSSLFNALA-KKDVAIVTD 249
AGK++L N LA + ++T
Sbjct: 799 GAGKTTLLNVLAERVTTGVITG 820
>gnl|CDD|183003 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 29.0 bits (66), Expect = 2.2
Identities = 15/77 (19%), Positives = 28/77 (36%), Gaps = 17/77 (22%)
Query: 173 EADLDFSEEEDVQNFSSKEVLNDILF--------LKNDISSHISQGKLGEIIRNGYKIVI 224
+ ++ F LN++ F + +S I G+ K+ +
Sbjct: 321 KPEVTFPTTSTAAADQVSLTLNNVSFTYPDQPQPVLKGLSLQIKAGE---------KVAL 371
Query: 225 LGHSNAGKSSLFNALAK 241
LG + GKS+L L +
Sbjct: 372 LGRTGCGKSTLLQLLTR 388
>gnl|CDD|151679 pfam11237, DUF3038, Protein of unknown function (DUF3038). This
family of proteins with unknown function appear to be
restricted to Cyanobacteria.
Length = 171
Score = 29.2 bits (66), Expect = 2.3
Identities = 23/78 (29%), Positives = 33/78 (42%), Gaps = 11/78 (14%)
Query: 105 LRLANPGEFSRRAFENGKIDLLEAESLADLISS----ETEMQRRL--SMEGMSG-ELSSL 157
LR NP RR+ G + + EA +L +I + R+L +E MS E L
Sbjct: 49 LRCTNP---LRRSTRRGPLTVEEARALVLIICYLAKRLYPLIRQLLLLLEQMSSQEPPPL 105
Query: 158 YGQ-WIDKLTHIRSFIEA 174
Q + L RS I+
Sbjct: 106 QTQLLSEYLDRFRSLIQE 123
>gnl|CDD|183407 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 28.8 bits (65), Expect = 2.6
Identities = 35/116 (30%), Positives = 45/116 (38%), Gaps = 27/116 (23%)
Query: 203 ISSHISQG--KLGEIIRNGYKIVIL-GHSNAGKSSLFNAL---AKKDVAIVTDIPG---- 252
IS G L E +RN KI ++ G S GKSSL N L + V V+ G
Sbjct: 155 ISVETGIGLEALLEQLRN--KITVVAGPSGVGKSSLINRLIPDVELRVGKVSGKLGRGRH 212
Query: 253 TTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVENADLILLLKEI 308
TTR V +L G L +DT G + D L+ +L E
Sbjct: 213 TTRHVELFELPNGGLL---ADTPGFNQPD------------LDCSPRELAHYFPEA 253
>gnl|CDD|161762 TIGR00201, comF, comF family protein. This protein is found in
species that do (Bacillus subtilis, Haemophilus
influenzae) or do not (E. coli, Borrelia burgdorferi)
have described systems for natural transformation with
exogenous DNA. It is involved in competence for
transformation in Bacillus subtilis.
Length = 190
Score = 29.0 bits (65), Expect = 2.8
Identities = 17/55 (30%), Positives = 22/55 (40%), Gaps = 8/55 (14%)
Query: 334 TYTEEYDHLISSFTGEGLEELINKIKSILSNKFKKLPFSIP--------SHKRHL 380
TY E LIS F G E+I + S+LS K +P S +R
Sbjct: 40 TYNEPLKELISRFKFRGQAEIIRALASLLSLTVSKAYRDLPDVIVPVPLSKEREW 94
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes.
Length = 581
Score = 28.7 bits (64), Expect = 2.9
Identities = 38/186 (20%), Positives = 63/186 (33%), Gaps = 41/186 (22%)
Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDL-----DLEGYLVKISDT-- 274
I GH + GK++L AL +P + +TIDL L Y + D
Sbjct: 3 IATAGHVDHGKTTLLKALTGIAAD---RLPEEKKRGMTIDLGFAYFPLPDYRLGFIDVPG 59
Query: 275 ---------AGIRETDD---IVE-KEGIKRTFLEVENADLILLLKEINSKKEISFPKNID 321
AG D +V+ EG+ + + + +L + I D
Sbjct: 60 HEKFISNAIAGGGGIDAALLVVDADEGVM-----TQTGEHLAVLDLLGIPHTIVVITKAD 114
Query: 322 FI---FIGTKSDLYSTYTEEYDHL-------ISSFTGEGLEELINKIKSIL---SNKFKK 368
+ I Y L S+ TG+G+ EL ++K++L K +
Sbjct: 115 RVNEEEIKRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGIGELKKELKNLLESLDIKRIQ 174
Query: 369 LPFSIP 374
P +
Sbjct: 175 KPLRMA 180
>gnl|CDD|132307 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP kinase.
This enzyme transfers a phosphate from ATP to GMP,
yielding ADP and GDP.
Length = 180
Score = 28.6 bits (65), Expect = 3.0
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD 256
IVI G S GKS+L AL ++D + I TTR
Sbjct: 4 IVISGPSGVGKSTLVKALLEEDPNLKFSISATTRK 38
>gnl|CDD|182600 PRK10631, PRK10631, p-hydroxybenzoic acid efflux subunit AaeB;
Provisional.
Length = 652
Score = 28.5 bits (64), Expect = 3.3
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 12 STGALPSAISIIRLSGPSCFQVCEFI 37
S GAL S I+I+ L P F +F+
Sbjct: 456 SLGALASTINILVLDNPMTFHFSQFL 481
>gnl|CDD|184206 PRK13647, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 274
Score = 28.6 bits (64), Expect = 3.3
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 216 IRNGYKIVILGHSNAGKSSL---FNAL 239
I G K +LG + AGKS+L N +
Sbjct: 28 IPEGSKTALLGPNGAGKSTLLLHLNGI 54
>gnl|CDD|178968 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 28.5 bits (65), Expect = 3.3
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTR 255
IV+ G S AGKS+L AL ++D + + TTR
Sbjct: 8 IVLSGPSGAGKSTLVKALLERDPNLQLSVSATTR 41
>gnl|CDD|183415 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 28.5 bits (65), Expect = 3.4
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 343 ISSFTGEGLEELINKIKSILSN 364
IS+ TG+GL+EL+ + +L
Sbjct: 307 ISALTGQGLDELLYAVAELLEE 328
>gnl|CDD|184193 PRK13633, PRK13633, cobalt transporter ATP-binding subunit;
Provisional.
Length = 280
Score = 28.5 bits (64), Expect = 3.7
Identities = 11/27 (40%), Positives = 18/27 (66%), Gaps = 3/27 (11%)
Query: 216 IRNGYKIVILGHSNAGKSSL---FNAL 239
++ G +VILG + +GKS++ NAL
Sbjct: 33 VKKGEFLVILGRNGSGKSTIAKHMNAL 59
>gnl|CDD|163017 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The
TrbB protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbB
is a homolog of the vir system VirB11 ATPase, and the
Flp pilus sytem ATPase TadA.
Length = 299
Score = 28.6 bits (64), Expect = 3.7
Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 198 FLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGT 253
+++ I + + L E + I+++G + +GK++L NAL + I + P
Sbjct: 111 YVEAGIMTAAQRDVLREAVLARKNILVVGGTGSGKTTLANALLAE---IAKNDPTD 163
>gnl|CDD|133958 PHA01753, PHA01753, Holliday junction resolvase.
Length = 121
Score = 28.3 bits (63), Expect = 3.8
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 217 RNGYKIVILGHSNAGKSSLFNALAKKDVAIVT-DIPGTTRDVLTID 261
NG+K + + S GK +L + +A K+ I ++ T++DV+T+D
Sbjct: 20 SNGFKALRIPVSGTGKQALPDIIATKNNTIYPIEVKSTSKDVVTVD 65
>gnl|CDD|183416 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 28.3 bits (64), Expect = 4.0
Identities = 16/33 (48%), Positives = 18/33 (54%), Gaps = 5/33 (15%)
Query: 225 LGHSNAGKSSLFNAL--AKKDVAIVTDIPGTTR 255
LG NAGKS+ A+ AK VA D P TT
Sbjct: 165 LGLPNAGKSTFIRAVSAAKPKVA---DYPFTTL 194
>gnl|CDD|152975 pfam12541, DUF3737, Protein of unknown function (DUF3737). This
family of proteins is found in bacteria, archaea and
eukaryotes. Proteins in this family are typically
between 281 and 297 amino acids in length.
Length = 278
Score = 28.4 bits (64), Expect = 4.3
Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 6/62 (9%)
Query: 162 IDKLTHIR-SFIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGY 220
ID L I DL F E +V ++ I +KN +S I +GEII +
Sbjct: 212 IDNLVLENCILINTDLAF-EYSNVD----ADIKGWIDSVKNPLSGKIRADSIGEIILDET 266
Query: 221 KI 222
KI
Sbjct: 267 KI 268
>gnl|CDD|183001 PRK11153, metN, DL-methionine transporter ATP-binding subunit;
Provisional.
Length = 343
Score = 28.2 bits (64), Expect = 4.3
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 9/35 (25%)
Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSL 235
N++S HI G++ +I G S AGKS+L
Sbjct: 22 NNVSLHIPAGEIFGVI---------GASGAGKSTL 47
>gnl|CDD|150775 pfam10139, Virul_Fac, Putative bacterial virulence factor. Members
of this family of prokaryotic proteins include various
putative virulence factor effector proteins. Their exact
function is, as yet, unknown.
Length = 852
Score = 28.2 bits (63), Expect = 4.5
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 211 KLGEIIRNGYKIVILGHSNAGKSSLFNALA 240
+LG + G S AGKS L +ALA
Sbjct: 35 RLGAAADTPMSVGFFGPSQAGKSYLISALA 64
>gnl|CDD|128665 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 = 28.1 bits (62), Expect = 4.8
Identities = 16/90 (17%), Positives = 35/90 (38%), Gaps = 11/90 (12%)
Query: 219 GYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLD----LEGYLVKISDT 274
G I+I+G +GK++L ALA++ + V+ ID + + +
Sbjct: 2 GEVILIVGPPGSGKTTLARALARE-------LGPPGGGVIYIDGEDILEEVLDQLLLIIV 54
Query: 275 AGIRETDDIVEKEGIKRTFLEVENADLILL 304
G + + + + D+++L
Sbjct: 55 GGKKASGSGELRLRLALALARKLKPDVLIL 84
>gnl|CDD|131721 TIGR02673, FtsE, cell division ATP-binding protein FtsE. This
model describes FtsE, a member of the ABC transporter
ATP-binding protein family. This protein, and its
permease partner FtsX, localize to the division site. In
a number of species, the ftsEX gene pair is located next
to FtsY, the signal recognition particle-docking
protein.
Length = 214
Score = 28.0 bits (63), Expect = 4.9
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 10/51 (19%)
Query: 189 SKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNAL 239
SK + L D+S HI +G+ + + G S AGK++L L
Sbjct: 8 SKAYPGGVAALH-DVSLHIRKGEF---------LFLTGPSGAGKTTLLKLL 48
>gnl|CDD|182993 PRK11144, modC, molybdate transporter ATP-binding protein;
Provisional.
Length = 352
Score = 27.9 bits (63), Expect = 5.1
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 224 ILGHSNAGKSSLFNALA 240
I G S AGK+SL NA++
Sbjct: 29 IFGRSGAGKTSLINAIS 45
>gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast
Envelope Protein Translocase).
Length = 313
Score = 27.9 bits (62), Expect = 5.6
Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 1/95 (1%)
Query: 210 GKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLV 269
GKL E + I+++G GKSS N++ + +A V+ + + G+ +
Sbjct: 29 GKLKEEDVSSLTILVMGKGGVGKSSTVNSIIGERIATVSAFQSEGLRPMMVSRTRAGFTL 88
Query: 270 KISDTAGIRETDDIVEKE-GIKRTFLEVENADLIL 303
I DT G+ E I ++ I + FL + D++L
Sbjct: 89 NIIDTPGLIEGGYINDQAVNIIKRFLLGKTIDVLL 123
>gnl|CDD|128470 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 = 27.9 bits (63), Expect = 6.0
Identities = 23/62 (37%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLT--IDLDLEGYLVKISDTAGI 277
YK+V+LG GKS+L + V D T D I++D E L+ I DTAG
Sbjct: 1 YKLVVLGSGGVGKSALTIQFVQG--HFVDDYDPTIEDSYRKQIEIDGEVCLLDILDTAGQ 58
Query: 278 RE 279
E
Sbjct: 59 EE 60
>gnl|CDD|183414 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 27.5 bits (62), Expect = 6.5
Identities = 16/32 (50%), Positives = 20/32 (62%), Gaps = 5/32 (15%)
Query: 225 LGHSNAGKSSLFNAL--AKKDVAIVTDIPGTT 254
+G +AGKSSL +AL AK +A D P TT
Sbjct: 165 VGFPSAGKSSLISALSAAKPKIA---DYPFTT 193
>gnl|CDD|130344 TIGR01277, thiQ, thiamine ABC transporter, ATP-binding protein.
This model describes the energy-transducing ATPase
subunit ThiQ of the ThiBPQ thiamine (and thiamine
pyrophosphate) ABC transporter in several
Proteobacteria. This protein is found so far only in
Proteobacteria, and is found in complete genomes only if
the ThiB and ThiP subunits are also found.
Length = 213
Score = 27.5 bits (61), Expect = 6.8
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
+ +G + I+G S AGKS+L N +A
Sbjct: 21 VADGEIVAIMGPSGAGKSTLLNLIA 45
>gnl|CDD|131259 TIGR02204, MsbA_rel, ABC transporter, permease/ATP-binding protein.
This protein is related to a Proteobacterial ATP
transporter that exports lipid A and to eukaryotic
P-glycoproteins.
Length = 576
Score = 27.7 bits (62), Expect = 6.8
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 216 IRNGYKIVILGHSNAGKSSLFNAL 239
+R G + ++G S AGKS+LF L
Sbjct: 363 VRPGETVALVGPSGAGKSTLFQLL 386
>gnl|CDD|161779 TIGR00232, tktlase_bact, transketolase, bacterial and yeast. This
model is designed to capture orthologs of bacterial
transketolases. The group includes two from the yeast
Saccharomyces cerevisiae but excludes dihydroxyactetone
synthases (formaldehyde transketolases) from various
yeasts and the even more distant mammalian
transketolases. Among the family of thiamine
diphosphate-dependent enzymes that includes
transketolases, dihydroxyacetone synthases, pyruvate
dehydrogenase E1-beta subunits, and
deoxyxylulose-5-phosphate synthases, mammalian and
bacterial transketolases seem not to be orthologous.
Length = 653
Score = 27.4 bits (61), Expect = 7.1
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 5/44 (11%)
Query: 147 MEGMSGELSSLYGQW-IDKLTHI----RSFIEADLDFSEEEDVQ 185
EG+S E++SL G + KL + R I+ +D S EDV
Sbjct: 155 QEGISYEVASLAGHLKLGKLIVLYDSNRISIDGAVDGSFTEDVA 198
>gnl|CDD|163239 TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB
family. Type I protein secretion is a system in some
Gram-negative bacteria to export proteins (often
proteases) across both inner and outer membranes to the
extracellular medium. This is one of three proteins of
the type I secretion apparatus. Targeted proteins are
not cleaved at the N-terminus, but rather carry signals
located toward the extreme C-terminus to direct type I
secretion. This model is related to models TIGR01842 and
TIGR01846, and to bacteriocin ABC transporters that
cleave their substrates during export.
Length = 694
Score = 27.5 bits (62), Expect = 7.5
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
IR G K+ I+G +GKS+L L
Sbjct: 488 IRPGEKVAIIGRIGSGKSTLLKLLL 512
>gnl|CDD|180635 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed.
Length = 284
Score = 27.4 bits (62), Expect = 8.1
Identities = 25/99 (25%), Positives = 39/99 (39%), Gaps = 16/99 (16%)
Query: 121 GKIDLL---EAESLA-DL-ISSE--TEMQRRLSMEGMSGELSSL-----YGQWIDKLTHI 168
++ L E E +A +L +S E EM+ RLS + S + G D L
Sbjct: 144 KRLGWLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDK 203
Query: 169 RSFIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHI 207
S L+ ED + + +L D L ++ S I
Sbjct: 204 SSDPADVLEEDNWEDQR----RALLADALEGLDERSRDI 238
>gnl|CDD|178750 PLN03211, PLN03211, ABC transporter G-25; Provisional.
Length = 659
Score = 27.2 bits (60), Expect = 8.9
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 219 GYKIVILGHSNAGKSSLFNALA 240
G + +LG S +GKS+L NALA
Sbjct: 94 GEILAVLGPSGSGKSTLLNALA 115
>gnl|CDD|149336 pfam08217, DUF1712, Fungal domain of unknown function (DUF1712).
The function of this family of proteins is unknown.
Length = 468
Score = 27.0 bits (60), Expect = 9.1
Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 171 FIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKI 222
F A +E++ ++ ++ + + L DI H+S+ GE N Y +
Sbjct: 313 FDPAFSKINEQDYLKELDAQ-LYPQLSLLYLDIEEHLSKEANGE---NAYDV 360
>gnl|CDD|177350 PHA02109, PHA02109, hypothetical protein.
Length = 233
Score = 26.9 bits (59), Expect = 9.8
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 12/74 (16%)
Query: 317 PKNIDFIFIGTKSDLYSTYTEEYDHLISSFTGEGLEELINKIKSI--LSNKFKKLPFSIP 374
PK ++ ++++ TE D + S TGE LE L +K+K I L+ K + L
Sbjct: 161 PKAVE---------IHAS-TERIDQVERSHTGENLEGLTDKLKQISELTIKLEALSDEAC 210
Query: 375 SHKRHLYHLSQTVR 388
K + +L V+
Sbjct: 211 QVKHKILNLRAEVK 224
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.318 0.138 0.385
Gapped
Lambda K H
0.267 0.0771 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 7,178,138
Number of extensions: 483488
Number of successful extensions: 1376
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1348
Number of HSP's successfully gapped: 113
Length of query: 440
Length of database: 5,994,473
Length adjustment: 96
Effective length of query: 344
Effective length of database: 3,920,105
Effective search space: 1348516120
Effective search space used: 1348516120
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 (21.7 bits)
S2: 59 (26.4 bits)