RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|255764471|ref|YP_003064835.2| GTP-binding protein EngA
[Candidatus Liberibacter asiaticus str. psy62]
(470 letters)
>gnl|CDD|178858 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 513 bits (1323), Expect = e-146
Identities = 181/464 (39%), Positives = 269/464 (57%), Gaps = 35/464 (7%)
Query: 4 TIAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAGIADG 63
+AIVG PNVGKSTLFNRL K+ A+V + PG+TRDR+YG+A G F ++DT GI
Sbjct: 3 VVAIVGRPNVGKSTLFNRLTGKRDAIVADTPGVTRDRIYGEAEWLGREFILIDTGGIEPD 62
Query: 64 KNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSNKMDT 123
+ KQ+ +Q ELAI EA +ILF++D +AG+TP D I LRK N P+I+V NK+D
Sbjct: 63 DD-GFEKQIREQAELAIEEADVILFVVDGRAGLTPADEEIAKILRKSNKPVILVVNKVDG 121
Query: 124 RIAQRNFYEIYSLDFKEIVEISAEHDLGTSELHSVIFKIFKQKYPNHPLEMIENNKRNEE 183
+ + YE YSL E ISAEH G +L L+ I EE
Sbjct: 122 PDEEADAYEFYSLGLGEPYPISAEHGRGIGDL----------------LDAILEELPEEE 165
Query: 184 SPKENITSEGKSSVKNISKPLRIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVS 243
E +P++IA++GRPNVGKS+LIN LLG R++ +G TRDS+
Sbjct: 166 EEDEE------------DEPIKIAIIGRPNVGKSSLINALLGEERVIVSDIAGTTRDSID 213
Query: 244 ISWNWKNHPIEIFDTAGMRKPSRITESLEQKTVKKSMQSVRTCETTIVLLDATIPFEKQD 303
+ + DTAG+R+ ++TE +E+ +V ++++++ + ++++DAT +QD
Sbjct: 214 TPFERDGQKYTLIDTAGIRRKGKVTEGVEKYSVIRTLKAIERADVVLLVIDATEGITEQD 273
Query: 304 LRIVDSVFNTGHAVVLALNKWDMVSDKL--NLLQDLRTKAIKNLPQIGDIYINTISGRTG 361
LRI G A+V+ +NKWD+V +K ++LR + LP + I IS TG
Sbjct: 274 LRIAGLALEAGRALVIVVNKWDLVDEKTMEEFKKELRRR----LPFLDYAPIVFISALTG 329
Query: 362 EGLDDLMVSVLEINKLWKTRITTSYLNSWLQKTQLQNPPPTIFNRYNRLKYITQIQSSPP 421
+G+D L+ ++ E + RI+TS LN L++ ++PPP + R ++KY TQ+ ++PP
Sbjct: 330 QGVDKLLEAIDEAYENANRRISTSVLNRVLEEAVERHPPPLVKGRRLKIKYATQVGTNPP 389
Query: 422 SFLIFCTFPNKIPESYKRYLINRLRINFSLSGIPIRMCFQSSKN 465
+F++F P +P SYKRYL N+LR F G PIR+ F+ KN
Sbjct: 390 TFVLFVNDPELLPFSYKRYLENQLREAFDFEGTPIRLEFREKKN 433
>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 = 495 bits (1278), Expect = e-141
Identities = 177/460 (38%), Positives = 267/460 (58%), Gaps = 35/460 (7%)
Query: 4 TIAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAGIADG 63
+AIVG PNVGKSTLFNRL K+ A+V + PG+TRDR YG A G F ++DT GI +
Sbjct: 1 VVAIVGRPNVGKSTLFNRLTGKRDAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGI-EE 59
Query: 64 KNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSNKMDT 123
+ + KQ+ +Q E+AI EA +ILF++D + G+TP D I +LRK P+I+V+NK+D
Sbjct: 60 DDDGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDEEIAKWLRKSGKPVILVANKIDG 119
Query: 124 RIAQRNFYEIYSLDFKEIVEISAEHDLGTSELHSVIFKIFKQKYPNHPLEMIENNKRNEE 183
+ E YSL F E + ISAEH G +L I ++
Sbjct: 120 KKEDAVAAEFYSLGFGEPIPISAEHGRGIGDLLDAILELL-------------------- 159
Query: 184 SPKENITSEGKSSVKNISKPLRIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVS 243
P+E E P++IA++GRPNVGKSTL+N LLG R++ +G TRDS+
Sbjct: 160 -PEEEEEEE------EEDGPIKIAIIGRPNVGKSTLVNALLGEERVIVSDIAGTTRDSID 212
Query: 244 ISWNWKNHPIEIFDTAGMRKPSRITESLEQKTVKKSMQSVRTCETTIVLLDATIPFEKQD 303
I + + DTAG+R+ ++TE +E+ +V ++++++ + +++LDAT +QD
Sbjct: 213 IPFERNGKKYLLIDTAGIRRKGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEGITEQD 272
Query: 304 LRIVDSVFNTGHAVVLALNKWDMVSD---KLNLLQDLRTKAIKNLPQIGDIYINTISGRT 360
LRI + G A+V+ +NKWD+V D + ++LR K LP + I IS T
Sbjct: 273 LRIAGLILEAGKALVIVVNKWDLVKDEKTREEFKKELRRK----LPFLDFAPIVFISALT 328
Query: 361 GEGLDDLMVSVLEINKLWKTRITTSYLNSWLQKTQLQNPPPTIFNRYNRLKYITQIQSSP 420
G+G+D L+ ++ E+ + RI+TS LN L++ +PPP + R ++KY TQ+ ++P
Sbjct: 329 GQGVDKLLDAIDEVYENANRRISTSKLNRVLEEAVAAHPPPLVNGRRLKIKYATQVGTNP 388
Query: 421 PSFLIFCTFPNKIPESYKRYLINRLRINFSLSGIPIRMCF 460
P+F++F P +P SYKRYL N+ R F G PIR+ F
Sbjct: 389 PTFVLFGNRPELLPFSYKRYLENQFREAFGFEGTPIRLEF 428
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 282 bits (723), Expect = 2e-76
Identities = 153/467 (32%), Positives = 230/467 (49%), Gaps = 58/467 (12%)
Query: 4 TIAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAG-IAD 62
+A+VG PNVGKSTL NR++ ++ AVV + PG+TRDR+ A NG F +VDT G D
Sbjct: 40 VVAVVGRPNVGKSTLVNRILGRREAVVEDVPGVTRDRVSYDAEWNGRRFTVVDTGGWEPD 99
Query: 63 GKNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSNKMD 122
K + + +Q E+A+ A +LF++D+ G T D A+ LR+ P+I+ +NK+D
Sbjct: 100 AK--GLQASVAEQAEVAMRTADAVLFVVDATVGATATDEAVARVLRRSGKPVILAANKVD 157
Query: 123 TRIAQRNFYEIYSLDFKEIVEISAEHDLGTSELHSVIFKIFKQKYPNHPLEMIENNKRNE 182
+ + ++SL E +SA H G +L + P
Sbjct: 158 DERGEADAAALWSLGLGEPHPVSALHGRGVGDLLDAVLAAL----P-------------- 199
Query: 183 ESPKENITSEGKSSVKNISKPLRIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSV 242
E P+ S G P R+A+VG+PNVGKS+L+N+L G R + +G T D V
Sbjct: 200 EVPRVGSASGG---------PRRVALVGKPNVGKSSLLNKLAGEERSVVDDVAGTTVDPV 250
Query: 243 SISWNWKNHPIEIFDTAGMRKPSRITESLEQKTVKKSMQSVRT------CETTIVLLDAT 296
DTAG+R+ + E S+RT E +VL+DA+
Sbjct: 251 DSLIELGGKTWRFVDTAGLRRRVKQASGHE------YYASLRTHAAIEAAEVAVVLIDAS 304
Query: 297 IPFEKQDLRIVDSVFNTGHAVVLALNKWDMV-SDKLNLL-----QDLRTKAIKNLPQIGD 350
P +QD R++ V G A+VLA NKWD+V D+ L ++L + P++
Sbjct: 305 EPISEQDQRVLSMVIEAGRALVLAFNKWDLVDEDRRYYLEREIDRELAQ--VPWAPRV-- 360
Query: 351 IYINTISGRTGEGLDDLMVSVLEINKLWKTRITTSYLNSWLQKTQLQNPPPTIFNRYNRL 410
IS +TG +D L+ ++ + W TRI T LN+WL + PPP + R+
Sbjct: 361 ----NISAKTGRAVDKLVPALETALESWDTRIPTGRLNAWLGELVAATPPPVRGGKQPRI 416
Query: 411 KYITQIQSSPPSFLIFCTFPNKIPESYKRYLINRLRINFSLSGIPIR 457
+ TQ + PP+F++F T + Y+R+L RLR F G PIR
Sbjct: 417 LFATQASTRPPTFVLFTT--GFLEAGYRRFLERRLRETFGFEGSPIR 461
>gnl|CDD|181925 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 268 bits (686), Expect = 2e-72
Identities = 139/463 (30%), Positives = 221/463 (47%), Gaps = 46/463 (9%)
Query: 4 TIAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAGI--- 60
+AIVG PNVGKSTL NR++ ++ AVV + PG+TRDR+ A G F +VDT G
Sbjct: 277 VVAIVGRPNVGKSTLVNRILGRREAVVEDTPGVTRDRVSYDAEWAGTDFKLVDTGGWEAD 336
Query: 61 ADGKNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSNK 120
+G + +IA Q ++A++ A ++F++D + G+T D I LR+ P+++ NK
Sbjct: 337 VEGIDSAIAS----QAQIAVSLADAVVFVVDGQVGLTSTDERIVRMLRRAGKPVVLAVNK 392
Query: 121 MDTRIAQRNFYEIYSLDFKEIVEISAEHDLGTSELHSVIFKIFKQKYPNHPLEMIENNKR 180
+D + ++ + E + L E ISA H G +L K
Sbjct: 393 IDDQASEYDAAEFWKLGLGEPYPISAMHGRGVGDLLDEALDSLKVA-------------- 438
Query: 181 NEESPKENITSEGKSSVKNISKPLRIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRD 240
K S S R+A+VGRPNVGKS+L+N+L R + +G TRD
Sbjct: 439 ----EKT-------SGFLTPSGLRRVALVGRPNVGKSSLLNQLTHEERAVVNDLAGTTRD 487
Query: 241 SVSISWNWKNHPIEIFDTAGMRKPSRITESLEQKTVKKSMQSVRTCETTIVLLDATIPFE 300
V DTAG+++ E + ++ ++ E + L DA+ P
Sbjct: 488 PVDEIVEIDGEDWLFIDTAGIKRRQHKLTGAEYYSSLRTQAAIERSELALFLFDASQPIS 547
Query: 301 KQDLRIVDSVFNTGHAVVLALNKWDMVS----DKLNLLQDLRTKAIKNLPQIGDIYINTI 356
+QDL+++ + G A+VL NKWD++ +L L + ++ +
Sbjct: 548 EQDLKVMSMAVDAGRALVLVFNKWDLMDEFRRQRLERLWKTEFDRVTWARRV------NL 601
Query: 357 SGRTGEGLDDLMVSVLEINKLWKTRITTSYLNSWLQKTQLQNPPPTIFNRYNRLKYITQI 416
S +TG + L ++ E + W RI T LN++L K Q ++P P + R+ + TQ
Sbjct: 602 SAKTGWHTNRLAPAMQEALESWDQRIPTGKLNAFLGKIQAEHPHPLRGGKQPRILFATQA 661
Query: 417 QSSPPSFLIFCT-FPNKIPESYKRYLINRLRINFSLSGIPIRM 458
+ PP F+IF T F + Y+R+L LR F G PI++
Sbjct: 662 STRPPRFVIFTTGF---LEHGYRRFLERSLREEFGFEGSPIQI 701
>gnl|CDD|179996 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 124 bits (313), Expect = 6e-29
Identities = 50/164 (30%), Positives = 87/164 (53%), Gaps = 7/164 (4%)
Query: 4 TIAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAGIADG 63
+ I G PNVGKS+L N L+ ++ A+V + G TRD + ++G+ ++DTAGI +
Sbjct: 217 KVVIAGRPNVGKSSLLNALLGEERAIVTDIAGTTRDVIEEHINLDGIPLRLIDTAGIRET 276
Query: 64 KNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSNKMDT 123
+ + K +++ AI EA L+L ++D+ +T D I L+ K P+I+V NK D
Sbjct: 277 DD-EVEKIGIERSREAIEEADLVLLVLDASEPLTEEDDEILEELKDK--PVIVVLNKAD- 332
Query: 124 RIAQRNFYEIYSLDFKEIVEISAEHDLGTSELHSVIFKIFKQKY 167
+ ++ + K ++ ISA+ G EL I ++ +
Sbjct: 333 -LTGEI--DLEEENGKPVIRISAKTGEGIDELREAIKELAFGGF 373
Score = 106 bits (268), Expect = 1e-23
Identities = 51/164 (31%), Positives = 89/164 (54%), Gaps = 18/164 (10%)
Query: 204 LRIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSISWNWKNHPIEIFDTAGMRK 263
L++ + GRPNVGKS+L+N LLG R + +G TRD + N P+ + DTAG+R+
Sbjct: 216 LKVVIAGRPNVGKSSLLNALLGEERAIVTDIAGTTRDVIEEHINLDGIPLRLIDTAGIRE 275
Query: 264 PSRITESLEQKTVKKSMQSVRTCETTIVLLDATIPFEKQDLRIVDSVFNTGHAVVLALNK 323
+ +E+ +++S +++ + +++LDA+ P ++D I++ + + VV LNK
Sbjct: 276 T---DDEVEKIGIERSREAIEEADLVLLVLDASEPLTEEDDEILEELKDKPVIVV--LNK 330
Query: 324 WDMVSDKLNLLQDLRTKAIKNLPQIGDIYINTISGRTGEGLDDL 367
D L ++ + P I IS +TGEG+D+L
Sbjct: 331 AD-------LTGEIDLEEENGKPVI------RISAKTGEGIDEL 361
>gnl|CDD|178854 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 117 bits (296), Expect = 6e-27
Identities = 63/167 (37%), Positives = 89/167 (53%), Gaps = 16/167 (9%)
Query: 5 IAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIING----VIFNIVDTAGI 60
+AIVG PNVGKSTL N LV +K+++V P TR R+ + I+ +IF VDT GI
Sbjct: 8 VAIVGRPNVGKSTLLNALVGQKISIVSPKPQTTRHRI--RGIVTEDDAQIIF--VDTPGI 63
Query: 61 ADGKNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSNK 120
K ++ + MN ++ + L+LF++D+ I P D I L+K P+I+V NK
Sbjct: 64 HKPKR-ALNRAMNKAAWSSLKDVDLVLFVVDADEKIGPGDEFILEKLKKVKTPVILVLNK 122
Query: 121 MDTRIAQRN----FYEIYS--LDFKEIVEISAEHDLGTSELHSVIFK 161
+D + + E S +DF EIV ISA EL VI K
Sbjct: 123 ID-LVKDKEELLPLLEELSELMDFAEIVPISALKGDNVDELLDVIAK 168
Score = 87.4 bits (218), Expect = 7e-18
Identities = 53/179 (29%), Positives = 81/179 (45%), Gaps = 39/179 (21%)
Query: 206 IAVVGRPNVGKSTLINRLLGY-------------NRLLTGSQSGI-TRDSVSISWNWKNH 251
+A+VGRPNVGKSTL+N L+G +R+ GI T D I
Sbjct: 8 VAIVGRPNVGKSTLLNALVGQKISIVSPKPQTTRHRIR-----GIVTEDDAQI------- 55
Query: 252 PIEIF-DTAGMRKP-SRITESLEQKTVKKSMQSVRTCETTIVLLDATIPFEKQDLRIVDS 309
IF DT G+ KP + ++ K S++ V + + ++DA D I++
Sbjct: 56 ---IFVDTPGIHKPKRALNRAM-NKAAWSSLKDV---DLVLFVVDADEKIGPGDEFILEK 108
Query: 310 VFNTGHAVVLALNKWDMVSDKLNLLQDLRTKAIKNLPQIGDIYINTISGRTGEGLDDLM 368
+ V+L LNK D+V DK LL + + L +I IS G+ +D+L+
Sbjct: 109 LKKVKTPVILVLNKIDLVKDKEELLP--LLEELSELMDFAEIV--PISALKGDNVDELL 163
>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 = 96.4 bits (240), Expect = 1e-20
Identities = 46/127 (36%), Positives = 78/127 (61%), Gaps = 2/127 (1%)
Query: 5 IAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAGIADGK 64
+AIVG+PNVGKS+L N L+K+ A+V + G TRD + G +NG++ ++DTAGI +
Sbjct: 206 LAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGILIKLLDTAGIREHA 265
Query: 65 NCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSNKMDTR 124
+ + + +++ AI +A L+++++D+ +T D I L K P I+V NK+D +
Sbjct: 266 D-FVERLGIEKSFKAIKQADLVIYVLDASQPLTKDDFLI-IDLNKSKKPFILVLNKIDLK 323
Query: 125 IAQRNFY 131
I F+
Sbjct: 324 INSLEFF 330
Score = 94.1 bits (234), Expect = 8e-20
Identities = 49/204 (24%), Positives = 93/204 (45%), Gaps = 12/204 (5%)
Query: 195 SSVKNISKPLRIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSISWNWKNHPIE 254
++ + ++A+VG PNVGKS+L+N LL +R + G TRD V + I+
Sbjct: 195 YKLEKLDDGFKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGILIK 254
Query: 255 IFDTAGMRKPSRITESLEQKTVKKSMQSVRTCETTIVLLDATIPFEKQDLRIVDSVFNTG 314
+ DTAG+R+ + + +E+ ++KS ++++ + I +LDA+ P K D I+D +
Sbjct: 255 LLDTAGIREHA---DFVERLGIEKSFKAIKQADLVIYVLDASQPLTKDDFLIIDLNKSK- 310
Query: 315 HAVVLALNKWDMVSDKLNLLQDLRTKAIKNLPQIGDIYINTISGRTGEGLDDLMVSVLEI 374
+L LNK D+ + L + N ++ + +D L +
Sbjct: 311 KPFILVLNKIDLKINSLEFFVSSKVLNSSN--------LSAKQLKIKALVDLLTQKINAF 362
Query: 375 NKLWKTRITTSYLNSWLQKTQLQN 398
+ + ++SW L+
Sbjct: 363 YSKERVELDDYLISSWQAMILLEK 386
>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 = 90.9 bits (226), Expect = 6e-19
Identities = 48/155 (30%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 2 IYTIAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVI--FNIVDTAG 59
I IVG PNVGKSTL NRL+ K + PG TR+ + +G FN++DTAG
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNK-FITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 59
Query: 60 IADGKNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSN 119
D + +I + E ++ +++ ++D + + I + N+PII+V N
Sbjct: 60 QEDYR--AIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIH-HAESNVPIILVGN 116
Query: 120 KMDTRIA------QRNFYEIYSLDFKEIVEISAEH 148
K+D R A F + L+ + I+ +SAE
Sbjct: 117 KIDLRDAKLKTHVAFLFAK---LNGEPIIPLSAET 148
Score = 68.5 bits (168), Expect = 3e-12
Identities = 49/165 (29%), Positives = 75/165 (45%), Gaps = 14/165 (8%)
Query: 205 RIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSV--SISWNWKNHPIEIFDTAGMR 262
+I +VG PNVGKSTL+NRLLG N+ +T + G TR+ V I + K + + DTAG
Sbjct: 3 KIVIVGDPNVGKSTLLNRLLG-NKFITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQE 61
Query: 263 KPSRITESLEQKTVKKSMQSVRTCETTIVLLDATIPFEKQDLRIVDSVFNTGHAVVLALN 322
I + S+R + I++LD EKQ I+ + ++L N
Sbjct: 62 DYRAIRRLYYRAVES----SLRVFDIVILVLDVEEILEKQTKEIIHHA-ESNVPIILVGN 116
Query: 323 KWDMVSDKLNLLQDLRTKAIKNLPQIGDIYINTISGRTGEGLDDL 367
K D+ L+T ++ I +S TG+ +D
Sbjct: 117 KIDLRD------AKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSA 155
>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 = 83.2 bits (206), Expect = 1e-16
Identities = 55/185 (29%), Positives = 89/185 (48%), Gaps = 14/185 (7%)
Query: 5 IAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIING---VIFNIVDTAGIA 61
+AI+G PNVGKSTL N+L +K+++ TR+R+ G G +IF +DT G
Sbjct: 3 VAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGI-HTTGASQIIF--IDTPGFH 59
Query: 62 DGKNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSNKM 121
+ K+ S+ + M + AI LILF++DS + + L+ P+++ NK+
Sbjct: 60 EKKH-SLNRLMMKEARSAIGGVDLILFVVDSDQW-NGDGEFVLTKLQNLKRPVVLTRNKL 117
Query: 122 DT-----RIAQRNFYEIYSLDFKEIVEISAEHDLGTSELHSVIFKIFKQKYPNHPLEMIE 176
D + + Y I DFK+IV ISA TS L + I + +P + +
Sbjct: 118 DNKFKDKLLPLIDKYAIL-EDFKDIVPISALTGDNTSFLAAFIEVHLPEGPFRYPEDYVT 176
Query: 177 NNKRN 181
+
Sbjct: 177 DQPDR 181
Score = 55.1 bits (133), Expect = 4e-08
Identities = 33/122 (27%), Positives = 56/122 (45%), Gaps = 4/122 (3%)
Query: 204 LRIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSISWNWKNHPIEIFDTAGMRK 263
+A++GRPNVGKSTL+N+L G +T ++ TR+ +S I DT G +
Sbjct: 1 GFVAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFIDTPGFHE 60
Query: 264 PSRITESLEQKTVKKSMQSVRTCETTIVLLDATIPFEKQDLRIVDSVFNTGHAVVLALNK 323
L K + ++ V + + ++D+ + ++ + N VVL NK
Sbjct: 61 KKHSLNRLMMKEARSAIGGV---DLILFVVDSD-QWNGDGEFVLTKLQNLKRPVVLTRNK 116
Query: 324 WD 325
D
Sbjct: 117 LD 118
>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 = 69.5 bits (171), Expect = 2e-12
Identities = 43/156 (27%), Positives = 70/156 (44%), Gaps = 33/156 (21%)
Query: 110 KNIPIIIVSNKMDTRIAQRNFYEIYSLDFKE----IVEISAEHDLGTSELHSVIFKIFKQ 165
N P +IV NK D +A + + F+E + I+A+ G ++ K+ K+
Sbjct: 47 GNKPRLIVLNKAD--LADPAVTKQWLKYFEEKGIKALAINAKKGKGVKKIIKAAKKLLKE 104
Query: 166 KYPNHPLEMIENNKRNEESPKENITSEGKSSVKNISKPLRIAVVGRPNVGKSTLINRLLG 225
K N++ + +N +P+R +VG PNVGKSTLINRL G
Sbjct: 105 K-----------NEKLKAKGLKN-------------RPIRAMIVGIPNVGKSTLINRLAG 140
Query: 226 YNRLLTGSQSGITRDSVSISWNWKNHPIEIFDTAGM 261
G++ G+T+ W + +E+ DT G+
Sbjct: 141 KKVAKVGNRPGVTK---GQQWIKLSDGLELLDTPGI 173
Score = 62.5 bits (153), Expect = 2e-10
Identities = 30/57 (52%), Positives = 35/57 (61%), Gaps = 5/57 (8%)
Query: 5 IAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIIN-GVIFNIVDTAGI 60
IVG PNVGKSTL NRL KK+A VGN PG+T+ GQ I ++DT GI
Sbjct: 121 AMIVGIPNVGKSTLINRLAGKKVAKVGNRPGVTK----GQQWIKLSDGLELLDTPGI 173
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 65.5 bits (159), Expect = 3e-11
Identities = 46/174 (26%), Positives = 91/174 (52%), Gaps = 6/174 (3%)
Query: 202 KPLRIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSISWNWKNHPIEIFDTAGM 261
K + + ++GRPN GKSTL+NR++G + + TR ++ K+ + ++DT G+
Sbjct: 51 KTVSVCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPGI 110
Query: 262 RKPSRITESLEQKTVKKSMQSVRTCETTIVLLDATIPFEKQDLRIVDSVFNTGHAVVLAL 321
+P SLE+ V+ + S+ + + ++++D+ F+ I+D + + + L
Sbjct: 111 FEPK---GSLEKAMVRCAWSSLHSADLVLLIIDSLKSFDDITHNILDKLRSLNIVPIFLL 167
Query: 322 NKWDMVSDKLNLLQDLRTKAIKNLPQIGDIYINTISGRTGEGLDDLMVSVLEIN 375
NK D+ S LN D++ +N P I+ +SG+ +GL + + S +I+
Sbjct: 168 NKIDIESKYLN---DIKAFLTENHPDSLLFPISALSGKNIDGLLEYITSKAKIS 218
Score = 58.6 bits (141), Expect = 3e-09
Identities = 40/119 (33%), Positives = 61/119 (51%), Gaps = 1/119 (0%)
Query: 4 TIAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAGIADG 63
++ I+G PN GKSTL NR++ +K+++V TR + G + + DT GI +
Sbjct: 54 SVCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPGIFEP 113
Query: 64 KNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSNKMD 122
K S+ K M +++ A L+L +IDS H I LR NI I + NK+D
Sbjct: 114 KG-SLEKAMVRCAWSSLHSADLVLLIIDSLKSFDDITHNILDKLRSLNIVPIFLLNKID 171
>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 = 62.8 bits (153), Expect = 2e-10
Identities = 48/175 (27%), Positives = 72/175 (41%), Gaps = 11/175 (6%)
Query: 9 GAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAGIADGKNCSI 68
G PNVGKSTLFN L VGN PG+T ++ G+ G IVD GI S+
Sbjct: 1 GNPNVGKSTLFNALTGAN-QTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFSL 59
Query: 69 AKQMNDQTELAINEAHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSNKMDTRIAQR 128
+++ + L + L++ ++D+ + +T L + IP+I+ N +D A++
Sbjct: 60 EEEVA-RDYLLNEKPDLVVNVVDASN--LERNLYLTLQLLELGIPMILALNLVD--EAEK 114
Query: 129 NFYEIYSLDFKEI-----VEISAEHDLGTSELHSVIFKIFKQKYPNHPLEMIENN 178
I +E V SA G L I K K I
Sbjct: 115 KGIRIDEEKLEERLGVPVVPTSATEGRGIERLKDAIRKAIGLKELKKRAIEIVPE 169
Score = 54.0 bits (130), Expect = 9e-08
Identities = 44/168 (26%), Positives = 78/168 (46%), Gaps = 12/168 (7%)
Query: 210 GRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSISWNWKNHPIEIFDTAGMRKPSRITE 269
G PNVGKSTL N L G N G+ G+T + ++ IEI D G+ S T
Sbjct: 1 GNPNVGKSTLFNALTGAN-QTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGIY--SLTTF 57
Query: 270 SLEQKTVKKSMQSVRTCETTIVLLDATIPFEKQDLRIVDSVFNTGHAVVLALNKWDMVSD 329
SLE++ + + + + + + ++DA+ E+ L + + G ++LALN D ++
Sbjct: 58 SLEEEVARDYLLNEKP-DLVVNVVDASN-LERN-LYLTLQLLELGIPMILALNLVDE-AE 113
Query: 330 KLNLLQDLRTKAIKNLPQIGDIYINTISGRTGEGLDDLMVSVLEINKL 377
K + D + L + + + S G G++ L ++ + L
Sbjct: 114 KKGIRID-----EEKLEERLGVPVVPTSATEGRGIERLKDAIRKAIGL 156
>gnl|CDD|181957 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 61.3 bits (150), Expect = 5e-10
Identities = 28/55 (50%), Positives = 34/55 (61%), Gaps = 5/55 (9%)
Query: 7 IVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIIN-GVIFNIVDTAGI 60
I+G PNVGKSTL NRL KK+A GN PG+T+ Q I G ++DT GI
Sbjct: 126 IIGIPNVGKSTLINRLAGKKIAKTGNRPGVTK----AQQWIKLGKGLELLDTPGI 176
Score = 60.6 bits (148), Expect = 9e-10
Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 200 ISKPLRIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSISWNWKNHPIEIFDTA 259
+ +R ++G PNVGKSTLINRL G TG++ G+T+ + W +E+ DT
Sbjct: 118 RPRAIRAMIIGIPNVGKSTLINRLAGKKIAKTGNRPGVTK---AQQWIKLGKGLELLDTP 174
Query: 260 GM 261
G+
Sbjct: 175 GI 176
>gnl|CDD|179035 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 58.2 bits (142), Expect = 4e-09
Identities = 46/183 (25%), Positives = 77/183 (42%), Gaps = 34/183 (18%)
Query: 5 IAIVGAPNVGKSTLFNRLV-KKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAGIAD- 62
IA G NVGKS+L N L +K +A PG T+ +IN F + D + D
Sbjct: 27 IAFAGRSNVGKSSLINALTNRKNLARTSKTPGRTQ-------LIN--FFEVNDKLRLVDL 77
Query: 63 ---G--KNCSIAKQMNDQTELAINE--------AHLILFLIDSKAGITPYDHAITSFLRK 109
G K ++K+ ++ + I E ++L LIDS+ + D + +L++
Sbjct: 78 PGYGYAK---VSKEEKEKWQKLIEEYLRTRENLKGVVL-LIDSRHPLKELDLQMIEWLKE 133
Query: 110 KNIPIIIVSNKMD--TR----IAQRNFYEIYSLDFKEIVEISAEHDLGTSELHSVIFKIF 163
IP++IV K D + + + E++ S+ G EL + I K
Sbjct: 134 YGIPVLIVLTKADKLKKGERKKQLKKVRKALKFGDDEVILFSSLKKQGIDELRAAIAKWL 193
Query: 164 KQK 166
+
Sbjct: 194 AEA 196
Score = 47.0 bits (113), Expect = 1e-05
Identities = 47/183 (25%), Positives = 75/183 (40%), Gaps = 45/183 (24%)
Query: 206 IAVVGRPNVGKSTLINRLLGYNRL-LTGSQSGITRDSVSISWNWKNHPIEIFDTAGMR-- 262
IA GR NVGKS+LIN L L T G T+ I N F+
Sbjct: 27 IAFAGRSNVGKSSLINALTNRKNLARTSKTPGRTQ---LI-----NF----FEVNDKLRL 74
Query: 263 ---------KPSRITESLEQKTVKKSMQSV-----RTCET---TIVLLDATIPFEKQDLR 305
K S K K+ Q + RT E ++L+D+ P ++ DL+
Sbjct: 75 VDLPGYGYAKVS--------KEEKEKWQKLIEEYLRTRENLKGVVLLIDSRHPLKELDLQ 126
Query: 306 IVDSVFNTGHAVVLALNKWDMVSDKLNL-LQDLRTKAIKNLPQIGDIYINTISGRTGEGL 364
+++ + G V++ L K +DKL + + K ++ + GD + S +G+
Sbjct: 127 MIEWLKEYGIPVLIVLTK----ADKLKKGERKKQLKKVRKALKFGDDEVILFSSLKKQGI 182
Query: 365 DDL 367
D+L
Sbjct: 183 DEL 185
>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 = 50.6 bits (122), Expect = 8e-07
Identities = 38/130 (29%), Positives = 62/130 (47%), Gaps = 22/130 (16%)
Query: 5 IAIVGAPNVGKSTLFNRLVK-KKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAGIAD- 62
IA G NVGKS+L N L KK+A PG T+ +IN F + D + D
Sbjct: 21 IAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQ-------LIN--FFEVNDGFRLVDL 71
Query: 63 -GKNCS-IAKQMNDQTELAINE--------AHLILFLIDSKAGITPYDHAITSFLRKKNI 112
G + ++K+ ++ + I E ++L L+D + + D + +LR++ I
Sbjct: 72 PGYGYAKVSKEEKEKWQKLIEEYLEKRENLKGVVL-LMDIRHPLKELDLEMLEWLRERGI 130
Query: 113 PIIIVSNKMD 122
P++IV K D
Sbjct: 131 PVLIVLTKAD 140
Score = 46.7 bits (112), Expect = 1e-05
Identities = 42/189 (22%), Positives = 68/189 (35%), Gaps = 59/189 (31%)
Query: 206 IAVVGRPNVGKSTLINRLLGYNRLL-TGSQSGITRDSVSISWNWKNHPIEIFDTAGMRKP 264
IA GR NVGKS+LIN L +L T G T+ I F+
Sbjct: 21 IAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQL------------INFFE------- 61
Query: 265 SRITESLE------------QKTVKKSMQSV-----RTCET---TIVLLDATIPFEKQDL 304
+ + K K+ Q + E ++L+D P ++ DL
Sbjct: 62 --VNDGFRLVDLPGYGYAKVSKEEKEKWQKLIEEYLEKRENLKGVVLLMDIRHPLKELDL 119
Query: 305 RIVDSVFNTGHAVVLALNKWDMVSDKLNLLQDLRTKAIKNLPQI--------GDIYINTI 356
+++ + G V++ L K +DKL +++ K L +I D +
Sbjct: 120 EMLEWLRERGIPVLIVLTK----ADKLK-----KSELNKQLKKIKKALKKDADDPSVQLF 170
Query: 357 SGRTGEGLD 365
S G+D
Sbjct: 171 SSLKKTGID 179
>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 = 46.7 bits (111), Expect = 1e-05
Identities = 24/127 (18%), Positives = 46/127 (36%), Gaps = 19/127 (14%)
Query: 5 IAIVGAPNVGKSTLFNRLVKKKMAVVGNHP--GITRDRLYGQAIINGVIFNIVDTAGIAD 62
+ ++G GKS+L ++LV + G T + + + +I D G
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEIPEEIQGDTLAVDTLEVDGDTELLHIWDFGG--- 58
Query: 63 GKNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHAITSFLR-------KKNIPII 115
+++ + + + A IL + D + + K IP+I
Sbjct: 59 ------REELKFEHIIFMKTADAILLVYDLTDRES-LNRVSRLIAWLPHLRKLGKKIPVI 111
Query: 116 IVSNKMD 122
+V NK D
Sbjct: 112 LVGNKFD 118
Score = 29.7 bits (67), Expect = 1.6
Identities = 8/21 (38%), Positives = 16/21 (76%)
Query: 205 RIAVVGRPNVGKSTLINRLLG 225
++ V+G GKS+L+++L+G
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVG 21
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 46.1 bits (110), Expect = 2e-05
Identities = 43/142 (30%), Positives = 57/142 (40%), Gaps = 34/142 (23%)
Query: 4 TIAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVI---FNIVD---- 56
I VG NVGKSTL L KK+ VG PG+TR N F + D
Sbjct: 11 EIVFVGRSNVGKSTLVRELTGKKVR-VGKRPGVTRK-------PNHYDWGDFILTDLPGF 62
Query: 57 --TAGIADGKNCSIAKQMNDQTELAINEAHLILF---LIDSKA-----------GITPYD 100
+G+ I ++ E + A IL ++D K+ G P D
Sbjct: 63 GFMSGVPKEVQEKIKDEIVRYIE---DNADRILAAVLVVDGKSFIEIIERWEGRGEIPID 119
Query: 101 HAITSFLRKKNIPIIIVSNKMD 122
+ FLR+ IP I+ NKMD
Sbjct: 120 VEMFDFLRELGIPPIVAVNKMD 141
Score = 40.3 bits (95), Expect = 0.001
Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 206 IAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSISW 246
I VGR NVGKSTL+ L G ++ G + G+TR W
Sbjct: 12 IVFVGRSNVGKSTLVRELTGK-KVRVGKRPGVTRKPNHYDW 51
>gnl|CDD|181981 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 44.3 bits (106), Expect = 6e-05
Identities = 19/34 (55%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 1 MIYTIAIVGAPNVGKSTLFNRLVKKKMAVVGNHP 34
M IVG PNVGKSTLFN L K A N+P
Sbjct: 1 MGLKCGIVGLPNVGKSTLFNALTKAG-AEAANYP 33
Score = 35.0 bits (82), Expect = 0.044
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 7/31 (22%)
Query: 204 LRIAVVGRPNVGKSTLINRLLGYNRLLTGSQ 234
L+ +VG PNVGKSTL N LT +
Sbjct: 3 LKCGIVGLPNVGKSTLFN-------ALTKAG 26
>gnl|CDD|181948 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 43.9 bits (104), Expect = 9e-05
Identities = 39/133 (29%), Positives = 63/133 (47%), Gaps = 8/133 (6%)
Query: 4 TIAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAGIADG 63
TI ++G PN GK+TLFN+L + VGN G+T +R GQ +VD G
Sbjct: 5 TIGLIGNPNSGKTTLFNQLTGARQR-VGNWAGVTVERKEGQFSTTDHQVTLVDLPGTYSL 63
Query: 64 KNCSIAKQMNDQTE---LAINEAHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSNK 120
S +++Q + +A L++ ++D A + +T L + IP I+ N
Sbjct: 64 TTISSQTSLDEQIACHYILSGDADLLINVVD--ASNLERNLYLTLQLLELGIPCIVALNM 121
Query: 121 MDTRIAQRNFYEI 133
+D IA++ I
Sbjct: 122 LD--IAEKQNIRI 132
Score = 39.7 bits (93), Expect = 0.002
Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 202 KPLRIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSISWNWKNHPIEIFDTAGM 261
K L I ++G PN GK+TL N+L G R G+ +G+T + ++ +H + + D G
Sbjct: 2 KKLTIGLIGNPNSGKTTLFNQLTG-ARQRVGNWAGVTVERKEGQFSTTDHQVTLVDLPGT 60
Query: 262 RKPSRITE--SLEQK 274
+ I+ SL+++
Sbjct: 61 YSLTTISSQTSLDEQ 75
>gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 41.0 bits (97), Expect = 6e-04
Identities = 30/130 (23%), Positives = 43/130 (33%), Gaps = 47/130 (36%)
Query: 110 KNIPIIIVSNKMDTRIAQRNFYEIYSLDFKEI----VEISAEHDLGTSELHSVIFKIFKQ 165
I IIV NK+D + ++ I +E+SA+ G EL ++
Sbjct: 110 NGIKPIIVLNKIDL-LDDLEEARELLALYRAIGYDVLELSAKEGEGLDELKPLL------ 162
Query: 166 KYPNHPLEMIENNKRNEESPKENITSEGKSSVKNISKPLRIAVVGRPNVGKSTLINRLLG 225
GK +V + G+ VGKSTL+N L
Sbjct: 163 --------------------------AGKVTV----------LAGQSGVGKSTLLNALAP 186
Query: 226 YNRLLTGSQS 235
L TG S
Sbjct: 187 DLELKTGEIS 196
>gnl|CDD|181982 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 40.2 bits (95), Expect = 0.001
Identities = 17/34 (50%), Positives = 20/34 (58%), Gaps = 5/34 (14%)
Query: 3 YTIAIVGAPNVGKSTLFNRLVKKKMAVV--GNHP 34
TI +VG PNVGKST FN +A V N+P
Sbjct: 2 ITIGLVGKPNVGKSTFFNAAT---LADVEIANYP 32
Score = 39.8 bits (94), Expect = 0.001
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 107 LRKKNIPIIIVSNKMDTRIAQRNFYEIYSLDFKEIVEISAEHDL 150
LRK + P++I +NK D A+ N + + +V SAE +L
Sbjct: 213 LRKISKPMVIAANKADLPPAEENIERLKEEKYYIVVPTSAEAEL 256
Score = 34.8 bits (81), Expect = 0.050
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 204 LRIAVVGRPNVGKSTLIN 221
+ I +VG+PNVGKST N
Sbjct: 2 ITIGLVGKPNVGKSTFFN 19
>gnl|CDD|184332 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 40.2 bits (95), Expect = 0.001
Identities = 45/184 (24%), Positives = 71/184 (38%), Gaps = 64/184 (34%)
Query: 113 PIIIVSNKMD--------TRIAQ--RNFYEIYSLDFKEIVEISAEHDLGTSELHSVIFKI 162
P+++V NK D ++ R + L ++V ISA+ G EL
Sbjct: 98 PVLLVGNKADLLPKSVKKNKVKNWLRQEAKELGLRPVDVVLISAQKGHGIDEL------- 150
Query: 163 FKQKYPNHPLEMIENNKRNEESPKENITSEGKSSVKNISKPLRIAVVGRPNVGKSTLINR 222
LE IE + + + VVG NVGKSTLINR
Sbjct: 151 ---------LEAIEKYREGRD----------------------VYVVGVTNVGKSTLINR 179
Query: 223 LL----GYNRLLTGSQ-SGITRDSVSISWNWKNHPIE----IFDTAGMRKPSRITESLEQ 273
++ G ++T S+ G T D + I P++ ++DT G+ ++ L
Sbjct: 180 IIKEITGEKDVITTSRFPGTTLDKIEI-------PLDDGSFLYDTPGIIHRHQMAHYLSA 232
Query: 274 KTVK 277
K +K
Sbjct: 233 KDLK 236
Score = 34.8 bits (81), Expect = 0.050
Identities = 22/64 (34%), Positives = 29/64 (45%), Gaps = 18/64 (28%)
Query: 7 IVGAPNVGKSTLFNRLVK-----KKMAVVGNHPGITRDRLY-----GQAIINGVIFNIVD 56
+VG NVGKSTL NR++K K + PG T D++ G + D
Sbjct: 165 VVGVTNVGKSTLINRIIKEITGEKDVITTSRFPGTTLDKIEIPLDDGSFLY--------D 216
Query: 57 TAGI 60
T GI
Sbjct: 217 TPGI 220
>gnl|CDD|185530 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 39.9 bits (94), Expect = 0.001
Identities = 18/35 (51%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 5 IAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRD 39
+ IVG PNVGKST FN L K++ N P T D
Sbjct: 24 MGIVGLPNVGKSTTFNALCKQQ-VPAENFPFCTID 57
Score = 34.5 bits (80), Expect = 0.064
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 204 LRIAVVGRPNVGKSTLINRL 223
L++ +VG PNVGKST N L
Sbjct: 22 LKMGIVGLPNVGKSTTFNAL 41
>gnl|CDD|179346 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 39.9 bits (94), Expect = 0.001
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 190 TSEGKSSVKNISKPLR-IAVVGRPNVGKSTLINRLLGYNRLLTG 232
EG + + +A++G VGKSTL+N LLG TG
Sbjct: 181 DGEGLDVLAAWLSGGKTVALLGSSGVGKSTLVNALLGEEVQKTG 224
Score = 33.0 bits (76), Expect = 0.18
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 4 TIAIVGAPNVGKSTLFNRL 22
T+A++G+ VGKSTL N L
Sbjct: 197 TVALLGSSGVGKSTLVNAL 215
Score = 29.9 bits (68), Expect = 1.5
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 7/51 (13%)
Query: 318 VLALNKWDMVSDKLNLLQDLRTKAIKNLPQIGDIYINTISGRTGEGLDDLM 368
V+ L K D+ D + ++ A +P + +S GEGLD L
Sbjct: 146 VIVLTKADLCEDAEEKIAEVEALAP-GVP------VLAVSALDGEGLDVLA 189
>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 = 39.7 bits (94), Expect = 0.002
Identities = 46/193 (23%), Positives = 73/193 (37%), Gaps = 60/193 (31%)
Query: 5 IAIVGAPNVGKSTLFNRL--VKKKMAVVGNHP--------GITRDRLYGQAIINGVIFNI 54
+ +VG PN GKSTL + + K K + ++P G+ R + +G F I
Sbjct: 160 VGLVGLPNAGKSTLISAVSAAKPK---IADYPFTTLVPNLGVVR-------VDDGRSFVI 209
Query: 55 VDTAGI----ADGKNCSIAKQMNDQTELA------INEAHLILFLID--SKAGITPYD-- 100
D G+ ++G L I ++L LID G P +
Sbjct: 210 ADIPGLIEGASEGAG------------LGHRFLKHIERTRVLLHLIDISPLDGRDPIEDY 257
Query: 101 HAITSFLRK-----KNIPIIIVSNKMDTRIAQRNFYEIYSLDF------KEIVEISAEHD 149
I + L+K P I+V NK+D + + E+ L K + ISA
Sbjct: 258 EIIRNELKKYSPELAEKPRIVVLNKIDL-LDEEELAEL--LKELKKALGKPVFPISALTG 314
Query: 150 LGTSELHSVIFKI 162
G EL + ++
Sbjct: 315 EGLDELLYALAEL 327
Score = 33.9 bits (79), Expect = 0.098
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 318 VLALNKWDMVSDKLNLLQDLRTKAIKNLPQIGDIYINTISGRTGEGLDDLMVSVLEI 374
++ LNK D++ + + + +K L + + IS TGEGLD+L+ ++ E+
Sbjct: 277 IVVLNKIDLLDE------EELAELLKELKKALGKPVFPISALTGEGLDELLYALAEL 327
Score = 33.2 bits (77), Expect = 0.15
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 206 IAVVGRPNVGKSTLINRL 223
+ +VG PN GKSTLI+ +
Sbjct: 160 VGLVGLPNAGKSTLISAV 177
>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 = 39.8 bits (94), Expect = 0.002
Identities = 44/183 (24%), Positives = 76/183 (41%), Gaps = 48/183 (26%)
Query: 205 RIAVVGRPNVGKSTLINRLLG---Y--NRLLTGSQSGITRDSVSISWNWKNHPIEIF-DT 258
+A+VG N GKSTL N L G Y ++L T D + + + + DT
Sbjct: 191 TVALVGYTNAGKSTLFNALTGADVYAADQLFA------TLDPTTRRLDLPDGGEVLLTDT 244
Query: 259 AG-MRK-PSRITESLEQKTVKKSMQSVRTCETTI---VLL---DATIPFEKQDLRIVDSV 310
G +R P + + ++ T E +LL DA+ P ++ + V+ V
Sbjct: 245 VGFIRDLPHELVAAF------RA-----TLEEVREADLLLHVVDASDPDREEQIEAVEKV 293
Query: 311 ---FNTGHA-VVLALNKWDMVSD-KLNLLQDLRTKAIKNLPQIGDIYINTISGRTGEGLD 365
+L NK D++ + ++ L++ +A+ +S +TGEGLD
Sbjct: 294 LEELGAEDIPQLLVYNKIDLLDEPRIERLEEGYPEAVF------------VSAKTGEGLD 341
Query: 366 DLM 368
L+
Sbjct: 342 LLL 344
Score = 39.8 bits (94), Expect = 0.002
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 2 IYTIAIVGAPNVGKSTLFNRLVKK 25
+ T+A+VG N GKSTLFN L
Sbjct: 189 VPTVALVGYTNAGKSTLFNALTGA 212
Score = 27.8 bits (63), Expect = 6.2
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 110 KNIPIIIVSNKMDTRIAQRNFYEIYSLDFKEIVEISAEHDLGTSEL 155
++IP ++V NK+D + + + + E V +SA+ G L
Sbjct: 300 EDIPQLLVYNKID-LLDEPRIERL-EEGYPEAVFVSAKTGEGLDLL 343
>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 = 39.5 bits (93), Expect = 0.002
Identities = 34/126 (26%), Positives = 57/126 (45%), Gaps = 16/126 (12%)
Query: 3 YTIAIVGAPNVGKSTLFNRLVKKKMAVVGNH-PGITRDRLYGQAIING--VIFNIVDTAG 59
Y + ++G+ VGKS L + V+ V ++ P I D Q I+G + +I+DTAG
Sbjct: 1 YKLVVLGSGGVGKSALTIQFVQGHF--VDDYDPTI-EDSYRKQIEIDGEVCLLDILDTAG 57
Query: 60 IADGKNCSIAKQMNDQTELAINEAHLILFLIDSK---AGITPYDHAITSFLRKKNIPIII 116
+ M DQ E L+++ I + I + I + ++PI++
Sbjct: 58 QEE------FSAMRDQYMRTG-EGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVL 110
Query: 117 VSNKMD 122
V NK D
Sbjct: 111 VGNKCD 116
>gnl|CDD|163008 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA.
This protein contains domains distinctive of a single
strand exonuclease (N-terminus, MobA/MobL, pfam03389) as
well as a helicase domain (central region, homologous to
the corresponding region of the F-type relaxase TraI,
TIGR02760). This protein likely fills the same role as
TraI(F), nicking (at the oriT site) and unwinding the
coiled plasmid prior to conjugative transfer.
Length = 744
Score = 38.6 bits (90), Expect = 0.003
Identities = 31/121 (25%), Positives = 53/121 (43%), Gaps = 28/121 (23%)
Query: 185 PKENITSEGKSSVKNISKPLRIA-VVGRPNVGKSTLIN------RLLGYNRL---LTG-- 232
++ E +V++++ IA VVGR GKST++ GY + L+G
Sbjct: 349 QHYRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTMLKAAREAWEAAGYRVIGAALSGKA 408
Query: 233 -----SQSGIT-RDSVSISWNWKN-------HPIEIFDTAGM---RKPSRITESLEQKTV 276
++SGI R S+ + W N + + D AGM R+ +R+ + E+
Sbjct: 409 AEGLQAESGIESRTLASLEYAWANGRDLLSDKDVLVIDEAGMVGSRQMARVLKEAEEAGA 468
Query: 277 K 277
K
Sbjct: 469 K 469
>gnl|CDD|183990 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 37.6 bits (88), Expect = 0.007
Identities = 32/142 (22%), Positives = 52/142 (36%), Gaps = 34/142 (23%)
Query: 2 IYTIAIVGAPNVGKSTLFNRLVKK-----KMAVVGNHPGIT--------RDRLYGQAII- 47
I I I+ + GK+TL R++ KM V G T ++R G I
Sbjct: 8 IRNIGILAHIDAGKTTLTERILFYTGKIHKMGEV--EDGTTVTDWMPQEQER--GITIES 63
Query: 48 -------NGVIFNIVDTAGIADGKNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYD 100
+ N++DT G D + E ++ + + D+ G+ P
Sbjct: 64 AATSCDWDNHRINLIDTPGHID---------FTGEVERSLRVLDGAVVVFDAVTGVQPQT 114
Query: 101 HAITSFLRKKNIPIIIVSNKMD 122
+ + IP +I NKMD
Sbjct: 115 ETVWRQADRYGIPRLIFINKMD 136
Score = 37.2 bits (87), Expect = 0.009
Identities = 37/157 (23%), Positives = 62/157 (39%), Gaps = 37/157 (23%)
Query: 206 IAVVGRPNVGKSTLINRLLGYNRLLTGS---------------------QSGITRDSVSI 244
I ++ + GK+TL R+L Y TG + GIT +S +
Sbjct: 11 IGILAHIDAGKTTLTERILFY----TGKIHKMGEVEDGTTVTDWMPQEQERGITIESAAT 66
Query: 245 SWNWKNHPIEIFDTAGMRKPSRITESLEQKTVKKSMQSVRTCETTIVLLDATIPFEKQDL 304
S +W NH I + DT G + E S+R + +V+ DA + Q
Sbjct: 67 SCDWDNHRINLIDTPGHIDFTGEVER-----------SLRVLDGAVVVFDAVTGVQPQTE 115
Query: 305 RIVDSVFNTGHAVVLALNKWDMV-SDKLNLLQDLRTK 340
+ G ++ +NK D V +D +L+D+ +
Sbjct: 116 TVWRQADRYGIPRLIFINKMDRVGADLFKVLEDIEER 152
>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 = 37.2 bits (87), Expect = 0.008
Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 8/76 (10%)
Query: 208 VVGRPNVGKSTLINRLLGYN----RLLTGSQ-SGITRDSVSISWNWKNHPIEIFDTAGMR 262
VVG NVGKS+LIN+LL N ++T S G T D + I + H ++DT G+
Sbjct: 159 VVGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLD-DGH--SLYDTPGII 215
Query: 263 KPSRITESLEQKTVKK 278
++ L++K +K
Sbjct: 216 NSHQMAHYLDKKDLKY 231
Score = 35.7 bits (83), Expect = 0.024
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 7 IVGAPNVGKSTLFNRLVK-----KKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAGIA 61
+VG NVGKS+L N+L+K K + PG T D + I ++ DT GI
Sbjct: 159 VVGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLI---EIPLDDGHSLYDTPGII 215
Query: 62 DGKN 65
+
Sbjct: 216 NSHQ 219
>gnl|CDD|162148 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.
Length = 763
Score = 36.5 bits (84), Expect = 0.013
Identities = 29/116 (25%), Positives = 47/116 (40%), Gaps = 7/116 (6%)
Query: 204 LRIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSISWNWKNHPIEIFDTAGMRK 263
L I V+G+ VGKS IN + G + T + T I + I + DT G+ K
Sbjct: 119 LNILVLGKSGVGKSATINSIFGEVKFSTDAFGMGTTSVQEIEGLVQGVKIRVIDTPGL-K 177
Query: 264 PSRITESLEQKTVKKSMQSVRTCETTIVLLDATIPFEKQD------LRIVDSVFNT 313
S +S +K + + ++ IVL + + +D LR + V
Sbjct: 178 SSASDQSKNEKILSSVKKFIKKNPPDIVLYVDRLDMQTRDSNDLPLLRTITDVLGP 233
>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 = 36.8 bits (85), Expect = 0.014
Identities = 34/188 (18%), Positives = 75/188 (39%), Gaps = 19/188 (10%)
Query: 206 IAVVGRPNVGKSTLINRLLGYN--RLLTGSQSGITRDSVSISWNWKNHPIEIFDTAGMRK 263
IA G + GK+TL+ L G RL + G+T D + ++ + D G
Sbjct: 3 IATAGHVDHGKTTLLKALTGIAADRLPEEKKRGMTIDLGFAYFPLPDYRLGFIDVPG--- 59
Query: 264 PSRITESLEQKTVKKSMQSVRTCETTIVLLDA---TIPFEKQDLRIVDSVFNTGHAVVLA 320
+K + ++ + ++++DA + + L ++D + ++
Sbjct: 60 --------HEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGI--PHTIVV 109
Query: 321 LNKWDMVSDKLNLLQDLRTKAIKN-LPQIGDIYINTISGRTGEGLDDLMVSVLEINKLWK 379
+ K D V+++ ++ K I N + + I S +TG+G+ +L + + +
Sbjct: 110 ITKADRVNEEEIKRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGIGELKKELKNLLESLD 169
Query: 380 TRITTSYL 387
+ L
Sbjct: 170 IKRIQKPL 177
>gnl|CDD|183415 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 36.6 bits (86), Expect = 0.015
Identities = 26/113 (23%), Positives = 44/113 (38%), Gaps = 9/113 (7%)
Query: 85 LILFLID--SKAGITPYD--HAITSFLRKKNI-----PIIIVSNKMDTRIAQRNFYEIYS 135
+I+ +ID G P + I L+ N P I+V+NKMD A+ N E
Sbjct: 239 VIVHVIDMSGSEGRDPIEDYEKINKELKLYNPRLLERPQIVVANKMDLPEAEENLEEFKE 298
Query: 136 LDFKEIVEISAEHDLGTSELHSVIFKIFKQKYPNHPLEMIENNKRNEESPKEN 188
++ ISA G EL + ++ ++ E + + +E
Sbjct: 299 KLGPKVFPISALTGQGLDELLYAVAELLEETPEFPLEEEEVEEEVYYKFEEEE 351
Score = 33.5 bits (78), Expect = 0.10
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 206 IAVVGRPNVGKSTLINRL 223
+ +VG PNVGKSTL++ +
Sbjct: 161 VGLVGFPNVGKSTLLSVV 178
Score = 32.0 bits (74), Expect = 0.34
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 5 IAIVGAPNVGKSTLFNRL 22
+ +VG PNVGKSTL + +
Sbjct: 161 VGLVGFPNVGKSTLLSVV 178
Score = 31.6 bits (73), Expect = 0.45
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 9/51 (17%)
Query: 318 VLALNKWDMVSDKLNLLQDLRTKAIKNLPQIGDIYINTISGRTGEGLDDLM 368
++ NK D+ + NL ++ + K + I S TG+GLD+L+
Sbjct: 278 IVVANKMDLPEAEENL-EEFKEKLGPKVFPI--------SALTGQGLDELL 319
>gnl|CDD|183417 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 35.4 bits (83), Expect = 0.031
Identities = 39/197 (19%), Positives = 70/197 (35%), Gaps = 64/197 (32%)
Query: 5 IAIVGAPNVGKSTLFNRL--VKKKMAVVGNHP--------GITRDRLYGQ----AIINGV 50
+ +VG PN GKSTL + + K K + ++P G+ R + A I G+
Sbjct: 161 VGLVGLPNAGKSTLISAVSAAKPK---IADYPFTTLHPNLGVVR-VDDYKSFVIADIPGL 216
Query: 51 IFNIVDTAGIADGK-----------NCSIAKQMNDQTELAINEAHLILFLID--SKAGIT 97
I G ++G + +L L+D + +
Sbjct: 217 I------EGASEGAGLGHRFLKHIERTRL-----------------LLHLVDIEAVDPVE 253
Query: 98 PYDHAITSFLRK-----KNIPIIIVSNKMDT----RIAQRNFYEIYSLDFKEIVEISAEH 148
Y I + L K + P I+V NK+D ++ + + ISA
Sbjct: 254 DY-KTIRNELEKYSPELADKPRILVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVT 312
Query: 149 DLGTSELHSVIFKIFKQ 165
G EL ++++ ++
Sbjct: 313 GEGLDELLRALWELLEE 329
Score = 34.7 bits (81), Expect = 0.060
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 11/62 (17%)
Query: 318 VLALNKWDMVSDKLNLLQDLRTKAIKNLPQIGDIYINTISGRTGEGLDDLMVSVLEINKL 377
+L LNK D++ + ++ R K + IS TGEGLD+L + L
Sbjct: 275 ILVLNKIDLLDE-----EEEREKRAALELAALGGPVFLISAVTGEGLDEL------LRAL 323
Query: 378 WK 379
W+
Sbjct: 324 WE 325
Score = 32.7 bits (76), Expect = 0.22
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 209 VGRPNVGKSTLINRL 223
VG PN GKSTLI+ +
Sbjct: 164 VGLPNAGKSTLISAV 178
>gnl|CDD|172354 PRK13826, PRK13826, Dtr system oriT relaxase; Provisional.
Length = 1102
Score = 35.1 bits (81), Expect = 0.036
Identities = 28/102 (27%), Positives = 49/102 (48%), Gaps = 29/102 (28%)
Query: 187 ENITSEGKSSVKNISKPLRIA-VVGRPNVGKSTLIN------RLLGYNRLLTGS------ 233
++ E K+++++++ P RIA VVGR GK+T++ GY R++ G+
Sbjct: 380 ARLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMMKAAREAWEAAGY-RVVGGALAGKAA 438
Query: 234 -----QSGITRDSVSISWN--WK-------NHPIEIFDTAGM 261
++GI ++S SW W N + + D AGM
Sbjct: 439 EGLEKEAGIQSRTLS-SWELRWNQGRDQLDNKTVFVLDEAGM 479
>gnl|CDD|183014 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 34.8 bits (81), Expect = 0.042
Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 4/39 (10%)
Query: 192 EGKSSVKNISKPL----RIAVVGRPNVGKSTLINRLLGY 226
+GK+ ++ L RIA+VG GK++L+N LLG+
Sbjct: 361 DGKTLAGPLNFTLPAGQRIALVGPSGAGKTSLLNALLGF 399
>gnl|CDD|183416 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 34.8 bits (81), Expect = 0.043
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 318 VLALNKWDMVSDKLNLLQDLRTKAI-KNLPQIGDIYINTISGRTGEGLDDL 367
L NK D++ ++ + R KAI + L G +Y IS +G G+ +L
Sbjct: 279 WLVFNKIDLLDEEE---AEERAKAIVEALGWEGPVY--LISAASGLGVKEL 324
Score = 27.9 bits (63), Expect = 5.4
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 209 VGRPNVGKSTLIN 221
+G PN GKST I
Sbjct: 165 LGLPNAGKSTFIR 177
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 34.7 bits (80), Expect = 0.048
Identities = 12/21 (57%), Positives = 17/21 (80%)
Query: 2 IYTIAIVGAPNVGKSTLFNRL 22
+ T+++VG N GKSTLFNR+
Sbjct: 197 VPTVSLVGYTNAGKSTLFNRI 217
Score = 28.1 bits (63), Expect = 5.2
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 206 IAVVGRPNVGKSTLINRL 223
+++VG N GKSTL NR+
Sbjct: 200 VSLVGYTNAGKSTLFNRI 217
>gnl|CDD|131089 TIGR02034, CysN, sulfate adenylyltransferase, large subunit.
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).
Length = 406
Score = 34.7 bits (80), Expect = 0.049
Identities = 50/196 (25%), Positives = 77/196 (39%), Gaps = 50/196 (25%)
Query: 204 LRIAVVGRPNVGKSTLINRLLGYNRLLTGSQ-SGITRDSVSISWNWKNHP---------- 252
LR G + GKSTLI RLL + + Q + + RDS K H
Sbjct: 1 LRFLTCGSVDDGKSTLIGRLLHDTKQIYEDQLAALERDS-------KKHGTQGGEIDLAL 53
Query: 253 ------------IEI------FDTAGMRKPSRI---TESLEQKTVKKSMQS-VRTCETTI 290
I I F T K I T EQ T ++M + T + +
Sbjct: 54 LVDGLQAEREQGITIDVAYRYFSTD---KRKFIVADTPGHEQYT--RNMATGASTADLAV 108
Query: 291 VLLDATIPFEKQDLR--IVDSVFNTGHAVVLALNKWDMVSDKLNLLQDLRTKAIKNLPQI 348
+L+DA +Q R + S+ H VVLA+NK D+V + ++++ + Q+
Sbjct: 109 LLVDARKGVLEQTRRHSYIASLLGIRH-VVLAVNKMDLVDYDEEVFENIKKDYLAFAEQL 167
Query: 349 G--DIYINTISGRTGE 362
G D+ +S G+
Sbjct: 168 GFRDVTFIPLSALKGD 183
>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.
Length = 368
Score = 34.0 bits (78), Expect = 0.083
Identities = 15/31 (48%), Positives = 15/31 (48%)
Query: 7 IVGAPNVGKSTLFNRLVKKKMAVVGNHPGIT 37
IVG PNVGKSTLF N P T
Sbjct: 7 IVGLPNVGKSTLFAATTNLLGNEAANPPFTT 37
>gnl|CDD|183406 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 33.3 bits (77), Expect = 0.13
Identities = 29/131 (22%), Positives = 47/131 (35%), Gaps = 49/131 (37%)
Query: 111 NIPIIIVSNKMD-----TRIAQRNFYEIY-SLDFKEIVEISAEHDLGTSELHSVIFKIFK 164
I +IV NK+D R +IY ++ ++ ++ +S+ G EL + +
Sbjct: 150 GIEPLIVLNKIDLLDDEGRAFVNEQLDIYRNIGYR-VLMVSSHTGEGLEELEAAL----- 203
Query: 165 QKYPNHPLEMIENNKRNEESPKENITSEGKSSVKNISKPLRIAVVGRPNVGKSTLINRLL 224
G+ S+ VG+ VGKS+LIN LL
Sbjct: 204 ---------------------------TGRISI----------FVGQSGVGKSSLINALL 226
Query: 225 GYNRLLTGSQS 235
+L G S
Sbjct: 227 PEAEILVGDVS 237
>gnl|CDD|163051 TIGR02868, CydC, thiol reductant ABC exporter, CydC 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.
Length = 529
Score = 33.5 bits (77), Expect = 0.13
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 205 RIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSIS 245
R+A++G GKSTL+ L G LL Q +T D VS+S
Sbjct: 363 RVAILGPSGSGKSTLLMLLTG---LLDPLQGEVTLDGVSVS 400
>gnl|CDD|150194 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 33.2 bits (76), Expect = 0.14
Identities = 29/134 (21%), Positives = 51/134 (38%), Gaps = 20/134 (14%)
Query: 4 TIAIVGAPNVGKSTLFNRLV--KKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAGIA 61
+ I G + GK++LF L + V P Y G ++D G
Sbjct: 5 AVIIAGLCDSGKTSLFTLLTTGSVRKTVTSQEPSAA----YKYMNNKGNSLTLIDFPG-- 58
Query: 62 DGKNCSIAKQMNDQTELAINEAHLILFLIDSKA---GITP-----YDHAITSFLRKKNIP 113
+ + ++ + T + ++F++DS A +T YD + L K I
Sbjct: 59 ---HVKLRYKLLE-TLKDSSSLRGLVFVVDSTAFPKEVTDTAEFLYDILSITELLKNGID 114
Query: 114 IIIVSNKMDTRIAQ 127
I+I NK + A+
Sbjct: 115 ILIACNKQEIFTAR 128
>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase. Mutations have
also been found that do not phosphorylate the
periplasmic binding proteins, yet still allow transport.
The ATPase activity of this protein seems to be
necessary, however.
Length = 300
Score = 33.2 bits (76), Expect = 0.15
Identities = 20/74 (27%), Positives = 25/74 (33%), Gaps = 15/74 (20%)
Query: 5 IAIVGAPNVGKSTLFNRLVK------KKMAVVGNHPGIT---------RDRLYGQAIING 49
+ I G P GKSTL L K+AV+ P R R+ A G
Sbjct: 37 VGITGTPGAGKSTLLEALGMELRRRGLKVAVIAVDPSSPFTGGSILGDRTRMQRLATDPG 96
Query: 50 VIFNIVDTAGIADG 63
+ T G G
Sbjct: 97 AFIRSMPTRGHLGG 110
Score = 30.1 bits (68), Expect = 1.3
Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 4/41 (9%)
Query: 187 ENITSEGKSSVKNIS----KPLRIAVVGRPNVGKSTLINRL 223
EN E K + I R+ + G P GKSTL+ L
Sbjct: 14 ENRHPEAKQLLDRIMPYTGNAHRVGITGTPGAGKSTLLEAL 54
>gnl|CDD|182472 PRK10454, PRK10454, PTS system N,N'-diacetylchitobiose-specific
transporter subunit IIA; Provisional.
Length = 115
Score = 32.9 bits (75), Expect = 0.17
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 11/59 (18%)
Query: 69 AKQMNDQTELAINEAHLILF-LIDSKAG----------ITPYDHAITSFLRKKNIPIII 116
AK M DQ+ +A+NEAHL+ LI+ G + DH +TS L ++ I +I
Sbjct: 50 AKAMMDQSRMALNEAHLVQTKLIEGDQGEGKMKVSLVLVHAQDHLMTSMLARELITELI 108
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. LepA (GUF1 in
Saccaromyces) is a GTP-binding membrane protein related
to EF-G and EF-Tu. Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including GUF1 of yeast) originated
within the bacterial LepA family. The function is
unknown.
Length = 595
Score = 32.7 bits (75), Expect = 0.20
Identities = 41/179 (22%), Positives = 76/179 (42%), Gaps = 36/179 (20%)
Query: 215 GKSTLINRLLGYNRLLTGSQ--------------SGITRDSVSISWNWK-----NHPIEI 255
GKSTL +RLL Y ++ + GIT + ++ N+K + + +
Sbjct: 15 GKSTLADRLLEYTGAISEREMREQVLDSMDLERERGITIKAQAVRLNYKAKDGETYVLNL 74
Query: 256 FDTAGMRKPSRITESLEQKTVKKSMQSVRTCETTIVLLDATIPFEKQDLRIVDSVFNTGH 315
DT P + S E V +S+ + CE ++L+DA E Q L V
Sbjct: 75 IDT-----PGHVDFSYE---VSRSLAA---CEGALLLVDAAQGIEAQTLANVYLALENDL 123
Query: 316 AVVLALNKWDMVSDKLNLLQDLRTKA-IKNLPQIGDIYINTISGRTGEGLDDLMVSVLE 373
++ +NK D+ S R K I+ + + S +TG G+++++ ++++
Sbjct: 124 EIIPVINKIDLPSADPE-----RVKKEIEEVIGLDASEAILASAKTGIGIEEILEAIVK 177
>gnl|CDD|162277 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor
regulator (CFTR). The model describes the cystis
fibrosis transmembrane conductor regulator (CFTR) in
eukaryotes. The principal role of this protein is
chloride ion conductance. The protein is predicted to
consist of 12 transmembrane domains. Mutations or lesions
in the genetic loci have been linked to the aetiology of
asthma, bronchiectasis, chronic obstructive pulmonary
disease etc. Disease-causing mutations have been studied
by 36Cl efflux assays in vitro cell cultures and
electrophysiology, all of which point to the impairment
of chloride channel stability and not the biosynthetic
processing per se.
Length = 1490
Score = 32.6 bits (74), Expect = 0.22
Identities = 22/62 (35%), Positives = 37/62 (59%), Gaps = 10/62 (16%)
Query: 190 TSEGKSSVKNISKPL----RIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSIS 245
T G++ ++++S + R+ ++GR GKSTL++ LL RLL+ ++ I D V S
Sbjct: 1228 TEAGRAVLQDLSFSVEGGQRVGLLGRTGSGKSTLLSALL---RLLS-TEGEIQIDGV--S 1281
Query: 246 WN 247
WN
Sbjct: 1282 WN 1283
>gnl|CDD|182996 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed.
Length = 635
Score = 32.6 bits (75), Expect = 0.23
Identities = 16/39 (41%), Positives = 25/39 (64%), Gaps = 6/39 (15%)
Query: 192 EGKSSVKNISKPL----RIAVVGRPN-VGKSTLINRLLG 225
+GK VK+ S + +IA++G PN GK+TL+ +LG
Sbjct: 330 DGKQLVKDFSAQVQRGDKIALIG-PNGCGKTTLLKLMLG 367
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation
releasing factor, RF-3 (prfC) was originally described
as stop codon-independent, in contrast to peptide chain
release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and
RF-2 are closely related to each other, while RF-3 is
similar to elongation factors EF-Tu and EF-G; RF-1 is
active at UAA and UAG and RF-2 is active at UAA and UGA.
More recently, RF-3 was shown to be active primarily at
UGA stop codons in E. coli. All bacteria and organelles
have RF-1. The Mycoplasmas and organelles, which
translate UGA as Trp rather than as a stop codon, lack
RF-2. RF-3, in contrast, seems to be rare among bacteria
and is found so far only in Escherichia coli and some
other gamma subdivision Proteobacteria, in Synechocystis
PCC6803, and in Staphylococcus aureus.
Length = 527
Score = 32.6 bits (74), Expect = 0.25
Identities = 31/143 (21%), Positives = 51/143 (35%), Gaps = 30/143 (20%)
Query: 4 TIAIVGAPNVGKST------LFNRLVKKKMAVVG---------------NHPGITRDRLY 42
T AI+ P+ GK+T L+ ++ AV G GI+
Sbjct: 13 TFAIISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGISITTSV 72
Query: 43 GQAIINGVIFNIVDTAGIADGKNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHA 102
Q + N++DT G D ++ T + L +ID+ G+
Sbjct: 73 MQFPYRDCLVNLLDTPGHED---------FSEDTYRTLTAVDNCLMVIDAAKGVETRTRK 123
Query: 103 ITSFLRKKNIPIIIVSNKMDTRI 125
+ R ++ PI NK+D I
Sbjct: 124 LMEVTRLRDTPIFTFMNKLDRDI 146
>gnl|CDD|173562 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 32.5 bits (74), Expect = 0.26
Identities = 31/125 (24%), Positives = 54/125 (43%), Gaps = 14/125 (11%)
Query: 3 YTIAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIING--VIFNIVDTAGI 60
Y + +VG VGKS L + ++ + + D Q +I+ + +I+DTAG
Sbjct: 6 YKLVVVGGGGVGKSALTIQFIQNHF--IDEYDPTIEDSYRKQCVIDEETCLLDILDTAGQ 63
Query: 61 ADGKNCSIAKQMNDQTELAINEAHLILFLIDSKAG---ITPYDHAITSFLRKKNIPIIIV 117
+ M DQ + + L ++ I S++ I + I K +P+I+V
Sbjct: 64 EE------YSAMRDQY-MRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILV 116
Query: 118 SNKMD 122
NK D
Sbjct: 117 GNKCD 121
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G.
Length = 689
Score = 32.1 bits (73), Expect = 0.36
Identities = 24/106 (22%), Positives = 46/106 (43%), Gaps = 12/106 (11%)
Query: 236 GITRDSVSISWNWKNHPIEIFDTAGMRKPSRITESLEQKTVKKSMQSVRTCETTIVLLDA 295
GIT S + + WK H I I DT P + ++E V++S+ R + + +LDA
Sbjct: 60 GITITSAATTVFWKGHRINIIDT-----PGHVDFTVE---VERSL---RVLDGAVAVLDA 108
Query: 296 TIPFEKQDLRIVDSVFNTGHAVVLALNKWD-MVSDKLNLLQDLRTK 340
+ Q + + +NK D ++ L ++ ++ +
Sbjct: 109 VGGVQPQSETVWRQANRYEVPRIAFVNKMDKTGANFLRVVNQIKQR 154
>gnl|CDD|163509 TIGR03797, NHPM_micro_ABC2, NHPM 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 propeptide
cleavage domain, and an HlyD homolog (TIGR03794). In a
number of genomes, a conserved propeptide sequence with
a classic Gly-Gly motif.
Length = 686
Score = 31.9 bits (73), Expect = 0.36
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 206 IAVVGRPNVGKSTLINRLLGYNRLLTGS 233
+A+VG GKSTL+ LLG+ +GS
Sbjct: 482 VAIVGPSGSGKSTLLRLLLGFETPESGS 509
Score = 29.2 bits (66), Expect = 2.5
Identities = 11/18 (61%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 5 IAIVGAPNVGKSTLFNRL 22
+AIVG GKSTL RL
Sbjct: 482 VAIVGPSGSGKSTLL-RL 498
>gnl|CDD|131368 TIGR02315, ABC_phnC, phosphonate ABC transporter, ATP-binding
protein. Phosphonates are a class of
phosphorus-containing organic compound with a stable
direct C-P bond rather than a C-O-P linkage. A number of
bacterial species have operons, typically about 14 genes
in size, with genes for ATP-dependent transport of
phosphonates, degradation, and regulation of the
expression of the system. Members of this protein family
are the ATP-binding cassette component of tripartite ABC
transporters of phosphonates.
Length = 243
Score = 31.5 bits (72), Expect = 0.43
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 193 GKSSVKNISKPLR----IAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSI 244
GK ++KNI+ + +A++G GKSTL+ + NRL+ S I + I
Sbjct: 14 GKQALKNINLNINPGEFVAIIGPSGAGKSTLLRCI---NRLVEPSSGSILLEGTDI 66
>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 = 31.5 bits (72), Expect = 0.46
Identities = 13/22 (59%), Positives = 17/22 (77%)
Query: 205 RIAVVGRPNVGKSTLINRLLGY 226
R+A+VG GKSTL+N LLG+
Sbjct: 350 RVALVGPSGAGKSTLLNLLLGF 371
>gnl|CDD|181855 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
Length = 332
Score = 31.3 bits (72), Expect = 0.60
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 204 LRIAVVGRPNVGKSTLINRL 223
LRI + G P VGKST I L
Sbjct: 57 LRIGITGVPGVGKSTFIEAL 76
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 31.1 bits (71), Expect = 0.62
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 204 LRIAVVGRPNVGKSTLINRLLGYNRLLTGSQ-SGITRDSV 242
LR G + GKSTLI RLL ++++ Q + + RDS
Sbjct: 25 LRFITCGSVDDGKSTLIGRLLYDSKMIFEDQLAALERDSK 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 = 31.2 bits (70), Expect = 0.65
Identities = 22/128 (17%), Positives = 45/128 (35%), Gaps = 7/128 (5%)
Query: 4 TIAIVGAPNVGKSTLF----NRLVKKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDTAG 59
I IVG P GK+TL L V+ + + Q ++ V +G
Sbjct: 4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSG 63
Query: 60 IADGKN-CSIAKQMNDQTELAINEAHLILFLIDSKAGI-TPYDHAITSFLRKKNIPIIIV 117
+ ++A+++ L ++E +L + + +KN+ +I+
Sbjct: 64 ELRLRLALALARKLKPDV-LILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILT 122
Query: 118 SNKMDTRI 125
+N
Sbjct: 123 TNDEKDLG 130
Score = 30.8 bits (69), Expect = 0.86
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 202 KPLRIAVVGRPNVGKSTLINRLLGY 226
I +VG P GK+TL L
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARE 25
>gnl|CDD|182733 PRK10790, PRK10790, putative multidrug transporter
membrane\ATP-binding components; Provisional.
Length = 592
Score = 30.8 bits (70), Expect = 0.68
Identities = 15/30 (50%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 199 NISKPLR--IAVVGRPNVGKSTLINRLLGY 226
N+S P R +A+VG GKSTL + L+GY
Sbjct: 361 NLSVPSRGFVALVGHTGSGKSTLASLLMGY 390
>gnl|CDD|182444 PRK10419, nikE, nickel transporter ATP-binding protein NikE;
Provisional.
Length = 268
Score = 30.8 bits (70), Expect = 0.80
Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 16/77 (20%)
Query: 190 TSEGKSSVKNISKPLR----IAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSIS 245
+ ++ + N+S L+ +A++GR GKSTL L+G L G
Sbjct: 21 KHQHQTVLNNVSLSLKSGETVALLGRSGCGKSTLARLLVG----LESPSQGNVS------ 70
Query: 246 WNWKNHPIEIFDTAGMR 262
W+ P+ + A +
Sbjct: 71 --WRGEPLAKLNRAQRK 85
>gnl|CDD|183055 PRK11247, ssuB, aliphatic sulfonates transport ATP-binding subunit;
Provisional.
Length = 257
Score = 30.8 bits (70), Expect = 0.87
Identities = 13/19 (68%), Positives = 15/19 (78%), Gaps = 1/19 (5%)
Query: 206 IAVVGRPNVGKSTLINRLL 224
+AVVGR GKSTL+ RLL
Sbjct: 41 VAVVGRSGCGKSTLL-RLL 58
>gnl|CDD|177605 PHA03368, PHA03368, DNA packaging terminase subunit 1; Provisional.
Length = 738
Score = 30.0 bits (68), Expect = 1.3
Identities = 29/86 (33%), Positives = 43/86 (50%), Gaps = 15/86 (17%)
Query: 298 PF---EKQDLRIVD---SVFNTGHAVVLALNKWDMVSDKLNLLQD---LRTKAIKNLPQI 348
PF +KQ D FN+G V+A ++VS+ + L D TK +KNL ++
Sbjct: 634 PFFLLQKQKTPAFDHFIKRFNSGR--VMA--SQELVSNTVRLQTDPVEYLTKQLKNLTEV 689
Query: 349 --GDIYINTISGRTGEGLDDLMVSVL 372
G T SG+ G DDLMV+++
Sbjct: 690 VTGGSDTRTFSGKRGGASDDLMVALV 715
>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
Provisional.
Length = 588
Score = 29.9 bits (68), Expect = 1.4
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 4 TIAIVGAPNVGKSTLFNRL 22
T+AIVG GKSTL N L
Sbjct: 363 TVAIVGPTGAGKSTLINLL 381
>gnl|CDD|162336 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. This
bacterial (and Arabidopsis) protein, termed TypA or
BipA, a GTP-binding protein, is phosphorylated on a
tyrosine residue under some cellular conditions. Mutants
show altered regulation of some pathways, but the
precise function is unknown.
Length = 594
Score = 30.0 bits (68), Expect = 1.6
Identities = 38/142 (26%), Positives = 57/142 (40%), Gaps = 36/142 (25%)
Query: 2 IYTIAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLY---------GQAII----- 47
I IAI+ + GK+TL + L+K+ + +R+ G I+
Sbjct: 1 IRNIAIIAHVDHGKTTLVDALLKQ--SGTFRANEAVAERVMDSNDLERERGITILAKNTA 58
Query: 48 ---NGVIFNIVDTAGIADGKNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHAIT 104
NG NIVDT G AD + E + +L L+D+ G P T
Sbjct: 59 IRYNGTKINIVDTPGHAD---------FGGEVERVLGMVDGVLLLVDASEGPMPQ----T 105
Query: 105 SFLRKKNI----PIIIVSNKMD 122
F+ KK + I+V NK+D
Sbjct: 106 RFVLKKALELGLKPIVVINKID 127
>gnl|CDD|181743 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 29.5 bits (67), Expect = 1.8
Identities = 9/21 (42%), Positives = 10/21 (47%)
Query: 3 YTIAIVGAPNVGKSTLFNRLV 23
+ I G P GKSTL L
Sbjct: 34 TIVGIAGPPGAGKSTLAEFLE 54
>gnl|CDD|177855 PLN02205, PLN02205, alpha,alpha-trehalose-phosphate synthase
[UDP-forming].
Length = 854
Score = 29.6 bits (66), Expect = 2.0
Identities = 31/99 (31%), Positives = 42/99 (42%), Gaps = 11/99 (11%)
Query: 356 ISGRTGEGLDDLMVSVLEINKLWKTRITTSYLNS-----WLQKTQLQNPPPTIFNRYNRL 410
+ GR L VSV NK++ RI +N W+ L P + R+NR+
Sbjct: 171 LGGRFNRSLWQAYVSV---NKIFADRIM-EVINPEDDFVWIHDYHLMVLPTFLRKRFNRV 226
Query: 411 KYITQIQSSPPSFLIFCTFPNKIPESYKRYLINRLRINF 449
K + S PS I+ T P I E R L+N I F
Sbjct: 227 KLGFFLHSPFPSSEIYKTLP--IREELLRALLNSDLIGF 263
>gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast
Envelope Protein Translocase).
Length = 313
Score = 29.5 bits (66), Expect = 2.0
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 14/67 (20%)
Query: 4 TIAIVGAPNVGKSTLFNRLVKKKMAVV------GNHPG-ITRDRLYGQAIINGVIFNIVD 56
TI ++G VGKS+ N ++ +++A V G P ++R R G NI+D
Sbjct: 40 TILVMGKGGVGKSSTVNSIIGERIATVSAFQSEGLRPMMVSRTR-------AGFTLNIID 92
Query: 57 TAGIADG 63
T G+ +G
Sbjct: 93 TPGLIEG 99
>gnl|CDD|149721 pfam08749, DUF1790, Family of unknown function (DUF1790). Family
of uncharacterized proteins ranging in length from 150
to 210 amino acids.
Length = 145
Score = 29.5 bits (67), Expect = 2.0
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 3/26 (11%)
Query: 425 IFCTFPNKIPESYKRYLINRL--RIN 448
+ C F K+PE KR + L IN
Sbjct: 48 LICYFDMKVPEG-KRPEVAELLNLIN 72
>gnl|CDD|183407 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 29.2 bits (66), Expect = 2.1
Identities = 17/33 (51%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 205 RIAVVGRPN-VGKSTLINRLLGYNRLLTGSQSG 236
+I VV P+ VGKS+LINRL+ L G SG
Sbjct: 173 KITVVAGPSGVGKSSLINRLIPDVELRVGKVSG 205
>gnl|CDD|183414 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 29.1 bits (66), Expect = 2.3
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 206 IAVVGRPNVGKSTLINRL 223
+ +VG P+ GKS+LI+ L
Sbjct: 162 VGLVGFPSAGKSSLISAL 179
>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 = 29.3 bits (66), Expect = 2.4
Identities = 22/79 (27%), Positives = 28/79 (35%), Gaps = 12/79 (15%)
Query: 205 RIAV-VGRPNVGKSTLINRLLGYNRLLTGSQSGI-------TRDSVSISWNWKNHPIEIF 256
RI+V G+ VGKS+LIN L + S T + H I
Sbjct: 121 RISVFAGQSGVGKSSLINALDPSVKQQVNDISSKLGLGKHTTTHVELFHF----HGGLIA 176
Query: 257 DTAGMRKPSRITESLEQKT 275
DT G + EQ T
Sbjct: 177 DTPGFNEFGLWHLEPEQLT 195
>gnl|CDD|179724 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 29.1 bits (66), Expect = 2.6
Identities = 9/25 (36%), Positives = 17/25 (68%)
Query: 1 MIYTIAIVGAPNVGKSTLFNRLVKK 25
M+ + + G P VGK+T+ N+ ++K
Sbjct: 1 MMKVVVVTGVPGVGKTTVLNKALEK 25
Score = 29.1 bits (66), Expect = 2.7
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 202 KPLRIAVVGRPNVGKSTLINRLL 224
+ V G P VGK+T++N+ L
Sbjct: 1 MMKVVVVTGVPGVGKTTVLNKAL 23
>gnl|CDD|184251 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 28.7 bits (65), Expect = 3.4
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 204 LRIAVVGRPNVGKSTLINRL 223
++I + G P VGK+TL+ ++
Sbjct: 1 MKIGITGPPGVGKTTLVLKI 20
>gnl|CDD|183107 PRK11376, hlyE, hemolysin E; Provisional.
Length = 303
Score = 28.5 bits (63), Expect = 3.6
Identities = 31/105 (29%), Positives = 45/105 (42%), Gaps = 13/105 (12%)
Query: 297 IPFEKQDLRIVDSVFNTGHAVVLALNKWDMVSDKLNLLQDLRTKAIKNLPQIGDIYINTI 356
IP K L+ V + F T V NK D+ + KL L ++ IG+I T
Sbjct: 208 IPELKNKLKSVQNFFTTLSNTVKQANK-DIDAAKLKLTTEIAA--------IGEIKTETE 258
Query: 357 SGRTGEGLDDLMVSVLE--INKLWKTRITTSYLNSWLQKTQLQNP 399
+ R DDLM+S+L+ K+ T Y +KT + P
Sbjct: 259 TTRFYVDYDDLMLSLLKEAAKKMINT--CNEYQKRHGKKTLFEVP 301
>gnl|CDD|183713 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 28.6 bits (65), Expect = 3.7
Identities = 21/88 (23%), Positives = 35/88 (39%), Gaps = 15/88 (17%)
Query: 48 NGVIFNIVDTAGIAD--GKNCSIAKQMNDQTELAINEAHLILFLIDSKAGITPYDHAITS 105
G N++DT G D G + E A+ + ++ + G+ P +
Sbjct: 58 KGHKINLIDTPGHVDFTG-----------EVERALRVLDGAVVVVCAVGGVEPQTETVWR 106
Query: 106 FLRKKNIPIIIVSNKMDTRIAQRNFYEI 133
K +P II NKMD A +F+ +
Sbjct: 107 QAEKYGVPRIIFVNKMDR--AGADFFRV 132
>gnl|CDD|183822 PRK12900, secA, preprotein translocase subunit SecA; Reviewed.
Length = 1025
Score = 28.6 bits (64), Expect = 3.8
Identities = 14/53 (26%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 130 FYEIYSLDFKEIVEISAEHDLGTSELHSVIFKIFKQKYPNHPLEMIENNKRNE 182
F+EIY LD +V I + ++ +++K ++KY L++ E K+ +
Sbjct: 550 FFEIYKLD---VVVIPTNKPIVRKDMDDLVYKTRREKYNAIVLKVEELQKKGQ 599
>gnl|CDD|185024 PRK15064, PRK15064, ABC transporter ATP-binding protein;
Provisional.
Length = 530
Score = 28.3 bits (64), Expect = 3.8
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 205 RIAVVGRPNVGKSTLINRLLG 225
R+A++G VGK+TL+ L+G
Sbjct: 347 RLAIIGENGVGKTTLLRTLVG 367
>gnl|CDD|185364 PRK15467, PRK15467, ethanolamine utilization protein EutP;
Provisional.
Length = 158
Score = 28.4 bits (63), Expect = 4.0
Identities = 17/37 (45%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 5 IAIVGAPNVGKSTLFN------RLVKKKMAVVGNHPG 35
IA VGA GK+TLFN L +K AV N G
Sbjct: 4 IAFVGAVGAGKTTLFNALQGNYTLARKTQAVEFNDKG 40
Score = 27.2 bits (60), Expect = 9.2
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 205 RIAVVGRPNVGKSTLINRLLGYNRLLTGSQS 235
RIA VG GK+TL N L G L +Q+
Sbjct: 3 RIAFVGAVGAGKTTLFNALQGNYTLARKTQA 33
>gnl|CDD|162008 TIGR00715, precor6x_red, precorrin-6x reductase. This enzyme was
found to be a monomer by gel filtration.
Length = 256
Score = 28.3 bits (63), Expect = 4.2
Identities = 18/77 (23%), Positives = 31/77 (40%), Gaps = 14/77 (18%)
Query: 236 GITRDSVSISWNWKNHPIEIFDTAGMRKPSR----------ITESLEQKTVKKSMQSVRT 285
G T DS +I+ IEI T + T +L+ + +++ ++
Sbjct: 7 GGTVDSRAIAKGLIAQGIEILVTVTTSEGKHLYPIHQALTVHTGALDPQELREFLKRHSI 66
Query: 286 CETTIVLLDATIPFEKQ 302
+L+DAT PF Q
Sbjct: 67 D----ILVDATHPFAAQ 79
>gnl|CDD|183433 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 28.4 bits (64), Expect = 4.4
Identities = 14/25 (56%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 201 SKP-LRIAVVGRPNVGKSTLINRLL 224
KP L +AV+G + GKSTL+ RLL
Sbjct: 3 EKPHLNLAVIGHVDHGKSTLVGRLL 27
>gnl|CDD|173382 PTZ00088, PTZ00088, adenylate kinase 1; Provisional.
Length = 229
Score = 28.2 bits (63), Expect = 4.5
Identities = 17/53 (32%), Positives = 24/53 (45%)
Query: 5 IAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVIFNIVDT 57
I + GAP VGK T L KK+ N I R+ + + I I +V +
Sbjct: 9 IVLFGAPGVGKGTFAEILSKKENLKHINMGNILREEIKAKTTIGKEIQKVVTS 61
>gnl|CDD|181426 PRK08444, PRK08444, hypothetical protein; Provisional.
Length = 353
Score = 28.1 bits (63), Expect = 4.7
Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 15/51 (29%)
Query: 134 YSLDFKEIVEISAEHD-LGTSELHSV--------------IFKIFKQKYPN 169
Y++ +EI+EI G E+H V IFK K+ YPN
Sbjct: 78 YTMSHEEILEIVKNSVKRGIKEVHIVSAHNPNYGYEWYLEIFKKIKEAYPN 128
>gnl|CDD|181229 PRK08099, PRK08099, bifunctional DNA-binding transcriptional
repressor/ NMN adenylyltransferase; Provisional.
Length = 399
Score = 28.1 bits (63), Expect = 4.9
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 4 TIAIVGAPNVGKSTLFNRL 22
T+AI+G + GKSTL N+L
Sbjct: 221 TVAILGGESSGKSTLVNKL 239
>gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein
MsbA. This family consists of a single polypeptide
chain transporter in the ATP-binding cassette (ABC)
transporter family, MsbA, which exports lipid A. It may
also act in multidrug resistance. Lipid A, a part of
lipopolysaccharide, is found in the outer leaflet of the
outer membrane of most Gram-negative bacteria. Members
of this family are restricted to the Proteobacteria
(although lipid A is more broadly distributed) and often
are clustered with lipid A biosynthesis genes.
Length = 571
Score = 28.1 bits (63), Expect = 4.9
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 205 RIAVVGRPNVGKSTLINRL 223
+A+VGR GKSTL+N +
Sbjct: 360 TVALVGRSGSGKSTLVNLI 378
>gnl|CDD|162386 TIGR01488, HAD-SF-IB, Haloacid Dehalogenase superfamily, subfamily
IB, phosphoserine phosphatase-like. Subfamily IA
includes the enzyme phosphoserine phosphatase
(TIGR00338) as well as three hypothetical equivalogs.
Many members of these hypothetical equivalogs have been
annotated as PSPase-like or PSPase-family proteins. In
particular, the hypothetical equivalog which appears to
be most closely related to PSPase contains only Archaea
(while TIGR00338 contains only eukaryotes and bacteria)
of which some are annotated as PSPases. Although this is
a reasonable conjecture, none of these sequences has
sufficient evidence for this assignment. If such should
be found, this model should be retired while the PSPase
model should be broadened to include these sequences.
Length = 177
Score = 28.1 bits (63), Expect = 5.0
Identities = 10/48 (20%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 90 IDSKAGITPYDHAITSFLRKKNIPIIIVSNKMDTRIAQRNFYEIYSLD 137
+ + + P + S+L+++ I +IVS D + E +D
Sbjct: 68 LARQVALRPGARELISWLKERGIDTVIVSGGFDFFV--EPVAEKLGID 113
>gnl|CDD|178789 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 28.2 bits (64), Expect = 5.0
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 236 GITRDSVSISWNWKNHPIEIFDTAG 260
GIT S + + WK+H I I DT G
Sbjct: 60 GITITSAATTCFWKDHRINIIDTPG 84
>gnl|CDD|182605 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
Provisional.
Length = 638
Score = 28.2 bits (63), Expect = 5.0
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 205 RIAVVGRPNVGKSTLINRLLG 225
RI ++GR GKSTLI L G
Sbjct: 340 RIGLLGRNGAGKSTLIKLLAG 360
>gnl|CDD|182528 PRK10535, PRK10535, macrolide transporter ATP-binding /permease
protein; Provisional.
Length = 648
Score = 28.2 bits (63), Expect = 5.3
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 5 IAIVGAPNVGKSTLFNRL 22
+AIVGA GKSTL N L
Sbjct: 37 VAIVGASGSGKSTLMNIL 54
>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 = 28.1 bits (63), Expect = 5.5
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 4 TIAIVGAPNVGKSTLFNRLVK 24
T+A+VG GKSTLF L++
Sbjct: 368 TVALVGPSGAGKSTLFQLLLR 388
>gnl|CDD|161745 TIGR00176, mobB, molybdopterin-guanine dinucleotide biosynthesis
protein MobB. This molybdenum cofactor biosynthesis
enzyme is similar to the urease accessory protein UreG
and to the hydrogenase accessory protein HypB, both GTP
hydrolases involved in loading nickel into the
metallocenters of their respective target enzymes.
Length = 155
Score = 28.1 bits (63), Expect = 5.5
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 206 IAVVGRPNVGKSTLINRLL 224
+ +VG N GK+TLI RL+
Sbjct: 2 LQIVGPKNSGKTTLIERLV 20
>gnl|CDD|183712 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 27.9 bits (63), Expect = 5.8
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 236 GITRDSVSISWNWKNHPIEIFDTAG 260
GIT S + + WK H I I DT G
Sbjct: 58 GITITSAATTCFWKGHRINIIDTPG 82
>gnl|CDD|183324 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
Reviewed.
Length = 556
Score = 27.8 bits (63), Expect = 5.8
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 3/21 (14%)
Query: 6 AIVG--APN-VGKSTLFNRLV 23
IVG PN GKSTLF +
Sbjct: 351 GIVGIIGPNGAGKSTLFKMIT 371
>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;
this model does not correctly align the sequences from
Methanococcus jannaschii and Pyrococcus horikoshii in
this region.
Length = 590
Score = 27.9 bits (62), Expect = 6.0
Identities = 16/70 (22%), Positives = 37/70 (52%), Gaps = 10/70 (14%)
Query: 299 FEKQDLRIVDSVFNTGHAVVLALNKWDMVSDKLNLLQDLRTKAIKNLPQIGDIYINTISG 358
F KQ++++ ++ + +V+ L++ +++ + + D TK + +P IS
Sbjct: 149 FSKQEIQVQQNLDTKVYNLVIKLHEEGFEAERFDRVTDF-TKTVAIIP---------ISA 198
Query: 359 RTGEGLDDLM 368
TGEG+ +L+
Sbjct: 199 ITGEGIPELL 208
Score = 27.1 bits (60), Expect = 9.5
Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 2/78 (2%)
Query: 83 AHLILFLIDSKAGITPYDHAITSFLRKKNIPIIIVSNKMDTRIAQRNFYEIYS-LDFKEI 141
A L + ++D G P + LR P ++ +NK+D RI +E ++
Sbjct: 93 ADLAILIVDINEGFKPQTQEALNILRMYKTPFVVAANKID-RIPGWRSHEGRPFMESFSK 151
Query: 142 VEISAEHDLGTSELHSVI 159
EI + +L T + VI
Sbjct: 152 QEIQVQQNLDTKVYNLVI 169
>gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein.
Length = 1394
Score = 27.8 bits (62), Expect = 6.0
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 7/80 (8%)
Query: 168 PNHPLEMIENNKRNEESPKENITSEGKSSVKNISKPLRIAVV-GRPNVGKSTLI----NR 222
PN L+++ R + ++ T + + + KP + VV GRP G STL+ +
Sbjct: 51 PNALLKILTRGFRKLKKFRDTKTFDILKPMDGLIKPGELTVVLGRPGSGCSTLLKTIASN 110
Query: 223 LLGYNRLLTG--SQSGITRD 240
G++ + G + GIT +
Sbjct: 111 TDGFHIGVEGVITYDGITPE 130
>gnl|CDD|150847 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 27.6 bits (62), Expect = 6.4
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 198 KNISKPLRIAVVGRPNVGKSTLINRLLGY 226
K +R + G GKS L+ + + Y
Sbjct: 18 DASKKVVRFVLTGERGSGKSVLLAQAMAY 46
>gnl|CDD|129256 TIGR00152, TIGR00152, dephospho-CoA kinase. This model produces
scores in the range of 0-25 bits against adenylate,
guanylate, uridine, and thymidylate kinases.
Length = 188
Score = 27.7 bits (62), Expect = 6.7
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 206 IAVVGRPNVGKSTLINRL 223
I + G GKST+ N L
Sbjct: 2 IGLTGGIGSGKSTVANYL 19
>gnl|CDD|147980 pfam06109, HlyE, Haemolysin E (HlyE). This family consists of
several enterobacterial haemolysin (HlyE)
proteins.Hemolysin E (HlyE) is a novel pore-forming
toxin of Escherichia coli, Salmonella typhi, and
Shigella flexneri. HlyE is unrelated to the well
characterized pore-forming E. coli hemolysins of the RTX
family, haemolysin A (HlyA), and the enterohaemolysin
encoded by the plasmid borne ehxA gene of E. coli 0157.
However, it is evident that expression of HlyE in the
absence of the RTX toxins is sufficient to give a
hemolytic phenotype in E. coli. HlyE is a protein of 34
kDa that is expressed during anaerobic growth of E.
coli. Anaerobic expression is controlled by the
transcription factor, FNR, such that, upon ingestion and
entry into the anaerobic mammalian intestine, HlyE is
produced and may then contribute to the colonisation of
the host.
Length = 299
Score = 27.7 bits (61), Expect = 7.0
Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 9/77 (11%)
Query: 297 IPFEKQDLRIVDSVFNTGHAVVLALNKWDMVSDKLNLLQDLRTKAIKNLPQIGDIYINTI 356
IP K+ L+ V F + A V NK D+ + KL L ++ IGDI T
Sbjct: 205 IPALKEKLKSVKDFFESLAATVKQANK-DIDAAKLKLKDEIAA--------IGDIKTETE 255
Query: 357 SGRTGEGLDDLMVSVLE 373
+ R DDLM+ +L+
Sbjct: 256 TTRFFVDYDDLMLKLLK 272
>gnl|CDD|179943 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 27.6 bits (62), Expect = 7.5
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 203 PLRIAVVGRPNVGKSTLINRLL 224
LR G + GKSTLI RLL
Sbjct: 27 LLRFLTCGSVDDGKSTLIGRLL 48
>gnl|CDD|162400 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. E. coli NadR has also
been found to regulate the import of its substrate,
nicotinamide ribonucleotide, but it is not known if the
other members of this model share that activity.
Length = 325
Score = 27.5 bits (61), Expect = 7.6
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 4 TIAIVGAPNVGKSTLFNRLVKK 25
T+AI+G + GKSTL N+L
Sbjct: 164 TVAILGGESTGKSTLVNKLAAV 185
>gnl|CDD|185016 PRK15056, PRK15056, manganese/iron transporter ATP-binding protein;
Provisional.
Length = 272
Score = 27.5 bits (61), Expect = 8.0
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 207 AVVGRPNVGKSTLINRLLGYNRLLTGS 233
A+VG GKSTL L+G+ RL +G
Sbjct: 37 ALVGVNGSGKSTLFKALMGFVRLASGK 63
>gnl|CDD|130260 TIGR01192, chvA, glucan exporter ATP-binding protein. This model
describes glucan exporter ATP binding protein in
bacteria. It belongs to the larger ABC transporter
superfamily with the characteristic ATP binding motif.
The In general, this protein is in some ways implicated
in osmoregulation and suggested to participate in the
export of glucan from the cytoplasm to periplasm. The
cyclic beta-1,2-glucan in the bactrerial periplasmic
space is suggested to confer the property of high
osmolority. It has also been demonstrated that mutants
in this loci have lost functions of virulence and
motility. It is unclear as to how virulence and
osmoadaptaion are related.
Length = 585
Score = 27.5 bits (61), Expect = 8.0
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 12/52 (23%)
Query: 4 TIAIVGAPNVGKSTLFNRLVKKKMAVVGNHPGITRDRLYGQAIINGVIFNIV 55
T+AIVG GK+TL N L + D GQ +I+G+ N V
Sbjct: 363 TVAIVGPTGAGKTTLINLLQR------------VYDPTVGQILIDGIDINTV 402
>gnl|CDD|150993 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 = 27.2 bits (61), Expect = 8.8
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 7/57 (12%)
Query: 5 IAIVGAPNVGKSTLFNRLVK-----KKMAVVGNHPGITRDRLYGQAIINGVIFNIVD 56
I IVG GK+ L+ A++ + G +R Y +I N +D
Sbjct: 18 ILIVGTTGTGKTQALRELLDQIRARGDRAIIYDPTGTFVERFYRPGG--DIILNPLD 72
>gnl|CDD|162130 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP)
Family protein.
Length = 617
Score = 27.3 bits (61), Expect = 9.0
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 194 KSSVKNISKPLR----IAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITR 239
K +KN+S + +AV+G GK+TL+N L R G + +
Sbjct: 38 KHLLKNVSGVAKPGELLAVMGSSGAGKTTLMNALA--FRSPKGVKGSGSV 85
>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 = 27.1 bits (61), Expect = 9.0
Identities = 14/38 (36%), Positives = 24/38 (63%), Gaps = 4/38 (10%)
Query: 192 EGKSSVKNIS---KP-LRIAVVGRPNVGKSTLINRLLG 225
+ ++ N+S +P ++A++GR GKSTL+ LLG
Sbjct: 476 QETPALDNVSLTIRPGEKVAIIGRIGSGKSTLLKLLLG 513
>gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit;
Provisional.
Length = 232
Score = 27.2 bits (61), Expect = 9.3
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 10/47 (21%)
Query: 205 RIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSISWNWKNH 251
R+A++G GKSTL+N + G+ +T S S++ N ++H
Sbjct: 27 RVAILGPSGAGKSTLLNLIAGF----------LTPASGSLTLNGQDH 63
>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 = 27.1 bits (60), Expect = 9.8
Identities = 11/39 (28%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 205 RIAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVS 243
+A++G GKSTL+N + G+ + + I + S
Sbjct: 26 IVAIMGPSGAGKSTLLNLIAGF---IEPASGSIKVNDQS 61
>gnl|CDD|184210 PRK13651, PRK13651, cobalt transporter ATP-binding subunit;
Provisional.
Length = 305
Score = 27.0 bits (60), Expect = 9.9
Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 13/79 (16%)
Query: 206 IAVVGRPNVGKSTLINRLLGYNRLLTGSQSGITRDSVSISWNWKNHPIEIFDTAGMRKPS 265
IA++G+ GK+T I L N LL +I W +K+ E K
Sbjct: 36 IAIIGQTGSGKTTFIEHL---NALLLPDTG-------TIEWIFKD---EKNKKKTKEKEK 82
Query: 266 RITESLEQKTVKKSMQSVR 284
+ + + QKT K ++ ++
Sbjct: 83 VLEKLVIQKTRFKKIKKIK 101
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
0.319 0.135 0.389
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 7,542,373
Number of extensions: 484296
Number of successful extensions: 1589
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1512
Number of HSP's successfully gapped: 185
Length of query: 470
Length of database: 5,994,473
Length adjustment: 97
Effective length of query: 373
Effective length of database: 3,898,497
Effective search space: 1454139381
Effective search space used: 1454139381
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 (26.5 bits)