RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780271|ref|YP_003064684.1| ATP-dependent protease
ATP-binding subunit ClpX [Candidatus Liberibacter asiaticus str.
psy62]
(424 letters)
>gnl|CDD|180029 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 815 bits (2107), Expect = 0.0
Identities = 294/413 (71%), Positives = 344/413 (83%), Gaps = 3/413 (0%)
Query: 6 NNGSVSKNALYCSFCGKSQHEVRKLIAGPTVFICDECVELCMDIIREENKSSITKSHEGI 65
G SK LYCSFCGKSQHEVRKLIAGP V+ICDEC+ELC +IIREE K + E +
Sbjct: 1 ARGGDSKKLLYCSFCGKSQHEVRKLIAGPGVYICDECIELCNEIIREELKEEAVELKE-L 59
Query: 66 PNPQEILRVLDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSN-VELAKSNILLVGPTGC 124
P P+EI LD+YVIGQ +AKKVL+VAV+NHYKRL H K + VEL KSNILL+GPTG
Sbjct: 60 PTPKEIKAHLDQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGS 119
Query: 125 GKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVERAQRGIVYI 184
GKT LAQTLARI+DVPF +ADATTLTEAGYVGEDVENI+LKLLQAADY+VE+AQRGIVYI
Sbjct: 120 GKTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQRGIVYI 179
Query: 185 DEVDKISRKSDNPSITRDVSGEGVQQALLKIMEGTIASVPPQGGRKHPQQEFLQVDTTNI 244
DE+DKI+RKS+NPSITRDVSGEGVQQALLKI+EGT+ASVPPQGGRKHPQQEF+QVDTTNI
Sbjct: 180 DEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPQQEFIQVDTTNI 239
Query: 245 LFICGGAFAGLDRIISARGEKASIGFSAVVKD-SDNRPVGEVLRNLESEDLVKFGLIPEF 303
LFICGGAF GL++II R K IGF A VK + R GE+L+ +E EDL+KFGLIPEF
Sbjct: 240 LFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLIKFGLIPEF 299
Query: 304 IGRLPVLATLEDLDENSLIRILSEPKNALIKQYQCLFDMEDVELVFHEDALREIARCAIA 363
IGRLPV+ATLE+LDE +L+RIL+EPKNAL+KQYQ LF+M+ VEL F ++AL IA+ AI
Sbjct: 300 IGRLPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIE 359
Query: 364 HKTGARGLRSILEKILLDTMFELPMLKGVSSVIISDDVVKGKACPLNVYTDRR 416
KTGARGLRSILE+ILLD MFELP + V V+I+ +VV+GKA PL +Y ++
Sbjct: 360 RKTGARGLRSILEEILLDVMFELPSREDVEKVVITKEVVEGKAKPLLIYREKS 412
>gnl|CDD|161849 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction.
Length = 413
Score = 625 bits (1613), Expect = e-180
Identities = 275/405 (67%), Positives = 330/405 (81%), Gaps = 11/405 (2%)
Query: 15 LYCSFCGKSQHEVRKLIAGPTVFICDECVELCMDIIREENKSSITKSH-------EGIPN 67
LYCSFCGKSQ EVRKLIAGP V+ICDEC+ELC DI+ EE + +P
Sbjct: 8 LYCSFCGKSQDEVRKLIAGPGVYICDECIELCHDILEEELGTRKESKEYEEEFELSYLPT 67
Query: 68 PQEILRVLDEYVIGQGQAKKVLAVAVHNHYKRLAHS--SKSSN-VELAKSNILLVGPTGC 124
P+EI LDEYVIGQ QAKKVL+VAV+NHYKRL KS N VEL+KSNILL+GPTG
Sbjct: 68 PKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGS 127
Query: 125 GKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVERAQRGIVYI 184
GKT LAQTLARI++VPF +ADATTLTEAGYVGEDVENI+LKLLQAADY+VE+AQ+GI+YI
Sbjct: 128 GKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQKGIIYI 187
Query: 185 DEVDKISRKSDNPSITRDVSGEGVQQALLKIMEGTIASVPPQGGRKHPQQEFLQVDTTNI 244
DE+DKISRKS+NPSITRDVSGEGVQQALLKI+EGT+A+VPPQGGRKHP QEF+Q+DT+NI
Sbjct: 188 DEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQEFIQIDTSNI 247
Query: 245 LFICGGAFAGLDRIISARGEKASIGFSAVVKDSDNRPVGEVLRNLESEDLVKFGLIPEFI 304
LFICGGAF GL++II R K+SIGF A VK ++ ++LR +E EDLVKFGLIPEFI
Sbjct: 248 LFICGGAFVGLEKIIKKRTGKSSIGFGAEVK-KKSKEKADLLRQVEPEDLVKFGLIPEFI 306
Query: 305 GRLPVLATLEDLDENSLIRILSEPKNALIKQYQCLFDMEDVELVFHEDALREIARCAIAH 364
GRLPV+ATLE LDE +LI IL++PKNAL+KQYQ LF M++VEL F E+AL+ IA+ A+
Sbjct: 307 GRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALER 366
Query: 365 KTGARGLRSILEKILLDTMFELPMLKGVSSVIISDDVVKGKACPL 409
KTGARGLRSI+E +LLD MF+LP L+ + V+I+ + V ++ PL
Sbjct: 367 KTGARGLRSIVEGLLLDVMFDLPSLEDLEKVVITKETVLKQSEPL 411
>gnl|CDD|179962 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 152 bits (386), Expect = 2e-37
Identities = 91/246 (36%), Positives = 117/246 (47%), Gaps = 60/246 (24%)
Query: 165 KLLQAADYNVERAQRGIVYIDEVDKISRKSDNPSITRDVSGEGVQQALLKIMEGTIASVP 224
++ Q A VE Q GIV+IDE+DKI+ + + DVS EGVQ+ LL ++EG+ S
Sbjct: 238 EIKQEAIERVE--QNGIVFIDEIDKIAARGGSSG--PDVSREGVQRDLLPLVEGSTVST- 292
Query: 225 PQGGRKHPQQEFLQVDTTNILFICGGAFAGLDRIISARGEKASIGFSAVVKDSDNRPVGE 284
K+ V T +ILFI GAF V K SD
Sbjct: 293 -----KYGM-----VKTDHILFIASGAFH-------------------VSKPSD------ 317
Query: 285 VLRNLESEDLVKFGLIPEFIGRLPVLATLEDLDENSLIRILSEPKNALIKQYQCLFDMED 344
LIPE GR P+ L+ L E +RIL+EPK +LIKQYQ L E
Sbjct: 318 --------------LIPELQGRFPIRVELDALTEEDFVRILTEPKASLIKQYQALLATEG 363
Query: 345 VELVFHEDALREIARCAIA--HKT---GARGLRSILEKILLDTMFELPMLKGVSSVIISD 399
V L F +DA+R IA A KT GAR L +++EK+L D FE P + G +V I
Sbjct: 364 VTLEFTDDAIRRIAEIAYQVNEKTENIGARRLHTVMEKLLEDISFEAPDMSG-ETVTIDA 422
Query: 400 DVVKGK 405
V K
Sbjct: 423 AYVDEK 428
Score = 101 bits (255), Expect = 3e-22
Identities = 47/112 (41%), Positives = 74/112 (66%), Gaps = 2/112 (1%)
Query: 68 PQEILRVLDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKT 127
P+EI+ LD+Y+IGQ AK+ +A+A+ N ++R+ + E+ NIL++GPTG GKT
Sbjct: 6 PREIVSELDKYIIGQDDAKRAVAIALRNRWRRM-QLPEELRDEVTPKNILMIGPTGVGKT 64
Query: 128 YLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVERAQR 179
+A+ LA++ + PF +AT TE GYVG DVE+II L++ A + R ++
Sbjct: 65 EIARRLAKLANAPFIKVEATKFTEVGYVGRDVESIIRDLVEIA-VKMVREEK 115
>gnl|CDD|116338 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 141 bits (358), Expect = 3e-34
Identities = 58/212 (27%), Positives = 82/212 (38%), Gaps = 62/212 (29%)
Query: 113 KSNILLVGPTGCGKTYLAQTLARIIDV---PFTMADATTLTEAGYVGEDVENIILKLLQA 169
+ L +GPTG GKT LA+ LA ++ D + E E+ + +L+ A
Sbjct: 3 IGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYME--------EHSVSRLIGA 54
Query: 170 ADYNVERAQRG------------IVYIDEVDKISRKSDNPSITRDVSGEGVQQALLKIME 217
V + G IV IDE++K GVQ LL+I+E
Sbjct: 55 PPGYVGYEEGGQLTEAVRRKPYSIVLIDEIEKAHP--------------GVQNDLLQILE 100
Query: 218 GTIASVPPQGGRKHPQQEFLQVDTTNILFICGGAFAGLDRIISARGEKASIGFSAVVKDS 277
G + + GR +VD N LFI G F ++R K+
Sbjct: 101 GGTLT--DKQGR--------KVDFRNTLFIMTGNFGSEKISDASRLGKSPD--------- 141
Query: 278 DNRPVGEVLRNLESEDLVKFGLIPEFIGRLPV 309
L DL+K G IPEF+GRLP+
Sbjct: 142 ------YELLKELVMDLLKKGFIPEFLGRLPI 167
>gnl|CDD|161852 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU, while
the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop ATP-binding
motif. Cys-287 of E. coli (position 308 in the seed
alignment), studied in PubMed:98389714, is Ser in other
members of the seed alignment.
Length = 441
Score = 124 bits (312), Expect = 5e-29
Identities = 87/253 (34%), Positives = 122/253 (48%), Gaps = 64/253 (25%)
Query: 158 DVENIILKLLQAADYNVERAQRGIVYIDEVDKISRKSDNPSITRDVSGEGVQQALLKIME 217
D E I + + A + Q GI++IDE+DKI++K ++ DVS EGVQ+ LL I+E
Sbjct: 233 DPEEIKQEAIDAVE------QSGIIFIDEIDKIAKKGESSG--ADVSREGVQRDLLPIVE 284
Query: 218 GTIASVPPQGGRKHPQQEFLQVDTTNILFICGGAFAGLDRIISARGEKASIGFSAVVKDS 277
G+ + K+ V T +ILFI GAF + K S
Sbjct: 285 GSTVNT------KYGM-----VKTDHILFIAAGAFQ-------------------LAKPS 314
Query: 278 DNRPVGEVLRNLESEDLVKFGLIPEFIGRLPVLATLEDLDENSLIRILSEPKNALIKQYQ 337
D LIPE GR P+ L+ L + RIL+EPKN+LIKQY+
Sbjct: 315 D--------------------LIPELQGRFPIRVELQALTTDDFERILTEPKNSLIKQYK 354
Query: 338 CLFDMEDVELVFHEDALREIARCA--IAHKT---GARGLRSILEKILLDTMFELPMLKGV 392
L E V + F ++A++ IA A + KT GAR L ++LE++L D FE P L G
Sbjct: 355 ALMKTEGVNIEFSDEAIKRIAELAYNVNEKTENIGARRLHTVLERLLEDISFEAPDLSG- 413
Query: 393 SSVIISDDVVKGK 405
++ I D V K
Sbjct: 414 QNITIDADYVSKK 426
Score = 99.1 bits (247), Expect = 2e-21
Identities = 47/103 (45%), Positives = 69/103 (66%), Gaps = 1/103 (0%)
Query: 68 PQEILRVLDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKT 127
P+EI+ LD+Y+IGQ AKK +A+A+ N Y+R ++ E+ NIL++GPTG GKT
Sbjct: 3 PREIVAELDKYIIGQDNAKKSVAIALRNRYRRS-QLNEELKDEVTPKNILMIGPTGVGKT 61
Query: 128 YLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAA 170
+A+ LA++ + PF +AT TE GYVG DVE+++ L AA
Sbjct: 62 EIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDLTDAA 104
>gnl|CDD|148346 pfam06689, zf-C4_ClpX, ClpX C4-type zinc finger. The ClpX heat
shock protein of Escherichia coli is a member of the
universally conserved Hsp100 family of proteins, and
possesses a putative zinc finger motif of the C4 type.
This presumed zinc binding domain is found at the
N-terminus of the ClpX protein. ClpX is an ATPase which
functions both as a substrate specificity component of
the ClpXP protease and as a molecular chaperone. The
molecular function of this domain is now known.
Length = 39
Score = 86.1 bits (214), Expect = 1e-17
Identities = 30/39 (76%), Positives = 34/39 (87%)
Query: 15 LYCSFCGKSQHEVRKLIAGPTVFICDECVELCMDIIREE 53
L CSFCGKSQ EV+KLIAGP V+ICDECVELC +I+ EE
Sbjct: 1 LRCSFCGKSQSEVKKLIAGPGVYICDECVELCYEILEEE 39
>gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA.
Length = 731
Score = 58.9 bits (143), Expect = 2e-09
Identities = 79/329 (24%), Positives = 126/329 (38%), Gaps = 83/329 (25%)
Query: 70 EILRVLDE----YVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCG 125
E L+ L++ + GQ +A L ++ KR + N + + L GPTG G
Sbjct: 443 EKLKNLEKNLKAKIFGQDEAIDSLVSSI----KRSRAGLGNPNKPVG--SFLFTGPTGVG 496
Query: 126 KTYLAQTLARIIDVPFTMADATTLTE-----------AGYVGEDVENIILKLLQAADYNV 174
KT LA+ LA + V D + E GYVG + LL A V
Sbjct: 497 KTELAKQLAEALGVHLERFDMSEYMEKHTVSRLIGAPPGYVGFEQGG----LLTEA---V 549
Query: 175 ERAQRGIVYIDEVDKISRKSDNPSITRDVSGEGVQQALLKIMEGTIASVPPQGGRKHPQQ 234
+ ++ +DE++K +P I LL++M+ A++ GRK +
Sbjct: 550 RKHPHCVLLLDEIEKA-----HPDIY---------NILLQVMDY--ATLTDNNGRKADFR 593
Query: 235 EFLQVDTTNILFICGGAFAGLDRIISARGEKASIGFSAVVKDSDNRPVGEVLRNLESEDL 294
+ + T+N AG + K IGF G +S+
Sbjct: 594 NVILIMTSN---------AGASEM-----SKPPIGF------------GSENVESKSDKA 627
Query: 295 VKFGLIPEFIGRLPVLATLEDLDENSLIRI----LSEPKNALIKQYQCLFDMEDVELVFH 350
+K PEF RL + L E L +I + E L ++ +++L
Sbjct: 628 IKKLFSPEFRNRLDAIIHFNPLSEEVLEKIVQKFVDELSKQLNEK--------NIKLELT 679
Query: 351 EDALREIARCAIAHKTGARGL-RSILEKI 378
+DA + +A + GAR L R I E+I
Sbjct: 680 DDAKKYLAEKGYDEEFGARPLARVIQEEI 708
Score = 32.7 bits (75), Expect = 0.20
Identities = 29/89 (32%), Positives = 43/89 (48%), Gaps = 16/89 (17%)
Query: 113 KSNILLVGPTGCGKTYLAQTLARII---DVP--------FTMADATTLTEAGYVGEDVEN 161
K+N LLVG G GKT +A+ LA I VP +++ + L Y G D E
Sbjct: 203 KNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLLAGTKYRG-DFE- 260
Query: 162 IILKLLQAADYNVERAQRGIVYIDEVDKI 190
+ L+A +E+ I++IDE+ I
Sbjct: 261 ---ERLKAVVSEIEKEPNAILFIDEIHTI 286
>gnl|CDD|151009 pfam10431, ClpB_D2-small, C-terminal, D2-small domain, of ClpB
protein. This is the C-terminal domain of ClpB protein,
referred to as the D2-small domain, and is a mixed
alpha-beta structure. Compared with the D1-small domain
(included in AAA, pfam00004) it lacks the long
coiled-coil insertion, and instead of helix C4 contains
a beta-strand (e3) that is part of a three stranded
beta-pleated sheet. In Thermophilus the whole protein
forms a hexamer with the D1-small and D2-small domains
located on the outside of the hexamer, with the long
coiled-coil being exposed on the surface. The D2-small
domain is essential for oligomerisation, forming a tight
interface with the D2-large domain of a neighbouring
subunit and thereby providing enough binding energy to
stabilize the functional assembly. The domain is
associated with two Clp_N, pfam02861, at the N-terminus
as well as AAA, pfam00004 and AAA_2, pfam07724.
Length = 89
Score = 52.8 bits (128), Expect = 2e-07
Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 7/86 (8%)
Query: 316 LDENSLIRILSEPKNALIKQYQCLFDMEDVELVFHEDALREIARCAIAHKTGARGLRSIL 375
L + L +I+ L + + L + + L + A +A + GAR LR +
Sbjct: 1 LSKEELRQIVDL---QLKRLQKRLAER-GITLELTDAAKDWLAEKGYDPEYGARPLRRAI 56
Query: 376 EKILLDTMFELP---MLKGVSSVIIS 398
++ + D + E LK +V +
Sbjct: 57 QREIEDPLAEEILSGELKEGDTVRVD 82
>gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 48.0 bits (114), Expect = 4e-06
Identities = 33/103 (32%), Positives = 53/103 (51%), Gaps = 9/103 (8%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVE 175
+LL GP G GKT LA+ +A F + + + Y GE E + ++ + A+ N
Sbjct: 215 VLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIM-SKYYGESEER-LREIFKEAEENAP 272
Query: 176 RAQRGIVYIDEVDKISRKSDNPSITRDVSGEGVQQALLKIMEG 218
I++IDE+D I+ K + +T +V V Q LL +M+G
Sbjct: 273 ----SIIFIDEIDAIAPKRE--EVTGEVEKRVVAQ-LLTLMDG 308
Score = 33.3 bits (76), Expect = 0.12
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVE 175
+LL GP G GKT LA+ +A F + + +VGE E I ++ + A
Sbjct: 490 VLLFGPPGTGKTLLAKAVATESGANFIAVRGPEIL-SKWVGES-EKAIREIFRKA----R 543
Query: 176 RAQRGIVYIDEVDKISRK 193
+A I++ DE+D I+
Sbjct: 544 QAAPAIIFFDEIDAIAPA 561
>gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 47.0 bits (113), Expect = 9e-06
Identities = 44/152 (28%), Positives = 65/152 (42%), Gaps = 43/152 (28%)
Query: 73 RVLDEYVIGQGQ---AKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYL 129
+ LDE V+GQ K L + RL S+++L GP G GKT L
Sbjct: 9 KTLDE-VVGQEHLLGPGKPLRRMIEAG--RL-------------SSMILWGPPGTGKTTL 52
Query: 130 AQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVERAQRGIVYIDEVDK 189
A+ +A D PF A T +G V +D+ +I + A +R I++IDE+ +
Sbjct: 53 ARIIAGATDAPFEALSAVT---SG-V-KDLREVI----EEARQRRSAGRRTILFIDEIHR 103
Query: 190 ISRKSDNPSITRDVSGEGVQQALLKIME-GTI 220
++ Q ALL +E GTI
Sbjct: 104 FNKAQ--------------QDALLPHVEDGTI 121
>gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 139
Score = 46.2 bits (110), Expect = 2e-05
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 115 NILLVGPTGCGKTYLAQTLARII--DVPFTMADATTLTEAGYVGE-DVENIILKLLQAAD 171
+LLVGP G GK+ LA+ LA + F + TE G ++ N +
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIANGTTSWVDGP- 59
Query: 172 YNVERAQRG-IVYIDEVDKISR 192
V A+ G I +DE+++ +
Sbjct: 60 -LVRAAREGEIAVLDEINRANP 80
>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 = 45.8 bits (108), Expect = 2e-05
Identities = 20/92 (21%), Positives = 34/92 (36%), Gaps = 11/92 (11%)
Query: 113 KSNILLVGPTGCGKTYLAQTLARIIDVP---FTMADATTLTEAGYVGEDVENIILKLLQA 169
IL+VGP G GKT LA+ LAR + P D + E + + K
Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61
Query: 170 ADYN--------VERAQRGIVYIDEVDKISRK 193
+ + + ++ +DE+ +
Sbjct: 62 SGELRLRLALALARKLKPDVLILDEITSLLDA 93
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 42.3 bits (99), Expect = 2e-04
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVE 175
+L+VGP G GKT LA+ +A VPF + E +VG + QA +
Sbjct: 188 VLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEM-FVGVGASRVRDMFEQA-----K 241
Query: 176 RAQRGIVYIDEVDKISRK 193
+A I++IDE+D + R+
Sbjct: 242 KAAPCIIFIDEIDAVGRQ 259
>gnl|CDD|182917 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 41.7 bits (98), Expect = 3e-04
Identities = 81/362 (22%), Positives = 135/362 (37%), Gaps = 86/362 (23%)
Query: 35 TVFICD-ECVELCMDIIREENKSSITKSHEGIPNPQEILRVLDE----YVIGQGQAKKVL 89
TV + D E V + I E++ S + + L+ L + V GQ +A + L
Sbjct: 420 TVNVADIESVVARIARIPEKSVSQSDR---------DTLKNLGDRLKMLVFGQDKAIEAL 470
Query: 90 AVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLARIIDVPFTMADATTL 149
A+ L H K + L GPTG GKT + L++ + + D +
Sbjct: 471 TEAIKMSRAGLGHEHKPV------GSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEY 524
Query: 150 TE-----------AGYVGEDVENIILKLLQAADYNVERAQRGIVYIDEVDKISRKSDNPS 198
E GYVG D LL A V + ++ +DE++K +P
Sbjct: 525 MERHTVSRLIGAPPGYVGFDQGG----LLTDA---VIKHPHAVLLLDEIEKA-----HPD 572
Query: 199 ITRDVSGEGVQQALLKIME-GTIASVPPQGGRKHPQQEFLQVDTTNILFICGGAFAGLDR 257
+ LL++M+ GT+ GRK + + V TTN AG+
Sbjct: 573 VF---------NLLLQVMDNGTLTD---NNGRKADFRNVVLVMTTN---------AGV-- 609
Query: 258 IISARGEKASIGFSAVVKDSDNRPVGEVLRNLESEDLVKFGLIPEFIGRLPVLATLEDLD 317
E+ SIG + +D+ + E +K PEF RL + + L
Sbjct: 610 ---RETERKSIGL--IHQDNSTDAMEE----------IKKIFTPEFRNRLDNIIWFDHLS 654
Query: 318 ENSLIRILSEPKNALIKQYQCLFDMEDVELVFHEDALREIARCAIAHKTGARGLRSILEK 377
++ + + I + Q D + V L ++A +A GAR + +++
Sbjct: 655 T----DVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPMARVIQD 710
Query: 378 IL 379
L
Sbjct: 711 NL 712
Score = 40.2 bits (94), Expect = 9e-04
Identities = 35/89 (39%), Positives = 46/89 (51%), Gaps = 16/89 (17%)
Query: 113 KSNILLVGPTGCGKTYLAQTLA-RII--DVPFTMADATT--------LTEAGYVGEDVEN 161
K+N LLVG +G GKT +A+ LA RI+ DVP MAD T L Y G D E
Sbjct: 207 KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRG-DFEK 265
Query: 162 IILKLLQAADYNVERAQRGIVYIDEVDKI 190
LL+ +E+ I++IDE+ I
Sbjct: 266 RFKALLK----QLEQDTNSILFIDEIHTI 290
>gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 41.3 bits (98), Expect = 5e-04
Identities = 35/121 (28%), Positives = 53/121 (43%), Gaps = 31/121 (25%)
Query: 75 LDEYVIGQGQAKKVLAVAVHNHYKR---LAHSSKSSNVELAKSNILLVGPTGCGKTYLAQ 131
LDE+ IGQ + K+ L + + KR L H +LL GP G GKT LA
Sbjct: 24 LDEF-IGQEKVKENLKIFIEAAKKRGEALDH-------------VLLYGPPGLGKTTLAN 69
Query: 132 TLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVERAQRGIVYIDEVDKIS 191
+A + V + L + G D+ IL L+ D +++IDE+ ++S
Sbjct: 70 IIANEMGVNIRITSGPALEKPG----DLAA-ILTNLEEGD---------VLFIDEIHRLS 115
Query: 192 R 192
Sbjct: 116 P 116
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 39.8 bits (93), Expect = 0.001
Identities = 30/101 (29%), Positives = 53/101 (52%), Gaps = 9/101 (8%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVE 175
+LL GP G GKT LA+ +A + F + L Y+GE ++ ++ + A E
Sbjct: 159 VLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRK-YIGEGAR-LVREIFELAK---E 213
Query: 176 RAQRGIVYIDEVDKISRKSDNPSITRDVSGEGVQQALLKIM 216
+A I++IDE+D I+ K + + D VQ+ L++++
Sbjct: 214 KAP-SIIFIDEIDAIAAKRTDSGTSGD---REVQRTLMQLL 250
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
RuvA specifically binds Holliday junctions as a sandwich
of two tetramers and maintains the configuration of the
junction. It forms a complex with two hexameric rings of
RuvB, the subunit that contains helicase activity. The
complex drives ATP-dependent branch migration of the
Holliday junction recombination intermediate. The
endonuclease RuvC resolves junctions.
Length = 305
Score = 38.0 bits (89), Expect = 0.004
Identities = 32/120 (26%), Positives = 55/120 (45%), Gaps = 25/120 (20%)
Query: 73 RVLDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQT 132
++L E+ IGQ + K+ L + + ++K L ++LL GP G GKT LA
Sbjct: 1 KLLAEF-IGQEKVKEQLQLFIE--------AAKMRQEAL--DHLLLYGPPGLGKTTLAHI 49
Query: 133 LARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVERAQRGIVYIDEVDKISR 192
+A + V + L + G D+ IL L+ D +++IDE+ ++S
Sbjct: 50 IANEMGVNLKITSGPALEKPG----DLAA-ILTNLEEGD---------VLFIDEIHRLSP 95
>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 = 37.4 bits (87), Expect = 0.007
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 116 ILLVGPTGCGKTYLAQTLARIID 138
+ ++GP+G GK+ L L ++D
Sbjct: 364 VAILGPSGSGKSTLLMLLTGLLD 386
>gnl|CDD|163223 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins.
Length = 852
Score = 36.5 bits (85), Expect = 0.013
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 16/66 (24%)
Query: 74 VLDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSN-----ILLVGPTGCGKTY 128
VL E V+GQ +A + ++ A+ + S L+ N L +GPTG GKT
Sbjct: 562 VLHERVVGQDEAVEAVSDAI-----------RRSRAGLSDPNRPIGSFLFLGPTGVGKTE 610
Query: 129 LAQTLA 134
LA+ LA
Sbjct: 611 LAKALA 616
Score = 29.9 bits (68), Expect = 1.2
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 19/88 (21%)
Query: 113 KSNILLVGPTGCGKTYLAQTLA-RII--DVPFTMAD--------ATTLTEAGYVGEDVEN 161
K+N +L+G G GKT + + LA RI+ DVP ++ + + A Y GE E
Sbjct: 194 KNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEER 253
Query: 162 I--ILKLLQAADYNVERAQRGIVYIDEV 187
+ +L + ++ + I++IDE+
Sbjct: 254 LKAVLNEVTKSEGQI------ILFIDEL 275
>gnl|CDD|182692 PRK10744, pstB, phosphate transporter ATP-binding protein;
Provisional.
Length = 260
Score = 36.5 bits (85), Expect = 0.014
Identities = 27/84 (32%), Positives = 47/84 (55%), Gaps = 12/84 (14%)
Query: 102 HSSKSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIIDV-PFTMADATTLTEAGYVGEDV 159
H+ K+ N+++AK+ + +GP+GCGK+ L +T R+ ++ P A+ G + D
Sbjct: 27 HALKNINLDIAKNQVTAFIGPSGCGKSTLLRTFNRMYELYPEQRAE-------GEILLDG 79
Query: 160 ENIILKLLQAADYNVERAQRGIVY 183
ENI L D + RA+ G+V+
Sbjct: 80 ENI---LTPKQDIALLRAKVGMVF 100
>gnl|CDD|178856 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase;
Reviewed.
Length = 307
Score = 35.9 bits (84), Expect = 0.022
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDV 139
I++VGPT GKT LA LA+ ++
Sbjct: 7 IVIVGPTASGKTALAIELAKRLNG 30
>gnl|CDD|162028 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock.
Length = 775
Score = 35.7 bits (83), Expect = 0.023
Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 20/88 (22%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFT------MADATTL-----TEAGYVGEDVENIIL 164
+ LVGP G GKT L +++A+ ++ F + D + T YVG II
Sbjct: 350 LCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRT---YVGAMPGRIIQ 406
Query: 165 KLLQAADYNVERAQRGIVYIDEVDKISR 192
L +A N + +DE+DKI
Sbjct: 407 GLKKAKTKN------PLFLLDEIDKIGS 428
>gnl|CDD|185633 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 35.5 bits (82), Expect = 0.027
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVE 175
+LL GP G GKT LA+ +A F + + Y+GE ++ + + A N
Sbjct: 182 VLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQK-YLGEG-PRMVRDVFRLARENAP 239
Query: 176 RAQRGIVYIDEVDKISRK 193
I++IDEVD I+ K
Sbjct: 240 ----SIIFIDEVDSIATK 253
>gnl|CDD|162266 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH.
Length = 495
Score = 35.3 bits (82), Expect = 0.032
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVE 175
+LLVGP G GKT LA+ +A VPF + E +VG + QA +
Sbjct: 91 VLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM-FVGVGASRVRDLFEQA-----K 144
Query: 176 RAQRGIVYIDEVDKISRK 193
+ I++IDE+D + R+
Sbjct: 145 KNAPCIIFIDEIDAVGRQ 162
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain.
Length = 499
Score = 35.2 bits (81), Expect = 0.036
Identities = 26/112 (23%), Positives = 39/112 (34%), Gaps = 24/112 (21%)
Query: 30 LIAGPTVFICDECVELCMDIIREENKSSITKSHEGIPNPQEILRVLDEY----VIGQGQA 85
LI G ++ D E+ + E + P + + + GQ A
Sbjct: 144 LIDGLNIYGADHLKEVV-KFL--EGSEKLPPRTNTKPKSIINKSYIIDLDLKDIKGQQHA 200
Query: 86 KKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLARII 137
K+ L +A + N+LL GP G GKT LA L I+
Sbjct: 201 KRALEIAAAGGH-----------------NLLLFGPPGSGKTMLASRLQGIL 235
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 34.8 bits (81), Expect = 0.039
Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 18/83 (21%)
Query: 114 SNILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAG------YVGEDVENIILKLL 167
+LL GP G GKT LA+ +A +AT + G ++GE ++ +L
Sbjct: 166 KGVLLYGPPGTGKTLLAKAVA-------HETNATFIRVVGSELVQKFIGEGAR-LVRELF 217
Query: 168 QAADYNVERAQRGIVYIDEVDKI 190
+ A E+A I++IDE+D I
Sbjct: 218 ELAR---EKAP-SIIFIDEIDAI 236
>gnl|CDD|184595 PRK14266, PRK14266, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 250
Score = 34.5 bits (79), Expect = 0.049
Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 87 KVLAVAVHNHYKRLAHSSKSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIIDV 139
+ V N Y AH K+ N+++ K+++ L+GP+GCGK+ +TL R+ D+
Sbjct: 2 YRIEVENLNTYFDDAHILKNVNLDIPKNSVTALIGPSGCGKSTFIRTLNRMNDL 55
>gnl|CDD|162029 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
Members of this family from Pyrococcus horikoshii and
Pyrococcus abyssi each contain a predicted intein.
Length = 608
Score = 34.4 bits (79), Expect = 0.054
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 21/78 (26%)
Query: 60 KSHEGIPNPQEILRVLDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLV 119
++ E IP P+ R++D+ VIGQ +A +++ A K N+LL+
Sbjct: 5 ETTEEIPVPE---RLIDQ-VIGQEEAVEIIKKAAKQ-----------------KRNVLLI 43
Query: 120 GPTGCGKTYLAQTLARII 137
G G GK+ LA+ +A ++
Sbjct: 44 GEPGVGKSMLAKAMAELL 61
>gnl|CDD|163401 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity.
Length = 512
Score = 34.3 bits (79), Expect = 0.062
Identities = 38/123 (30%), Positives = 50/123 (40%), Gaps = 36/123 (29%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEA-----------GYVGEDVENIIL 164
+LL GP GCGKT +A+ +A + + T YVGE I L
Sbjct: 219 VLLYGPPGCGKTLIAKAVAN--SLAQRIGAETGDKSYFLNIKGPELLNKYVGETERQIRL 276
Query: 165 KLLQAADYNVERAQRG---IVYIDEVDKISRKSDNPSITRDVSGEGVQQALLKIMEGTIA 221
+A E+A G IV+ DE+D I R TR G GV +E T+
Sbjct: 277 IFQRAR----EKASDGRPVIVFFDEMDSIFR-------TR---GSGVSSD----VETTV- 317
Query: 222 SVP 224
VP
Sbjct: 318 -VP 319
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728).
Length = 262
Score = 34.0 bits (78), Expect = 0.078
Identities = 13/23 (56%), Positives = 14/23 (60%)
Query: 118 LVGPTGCGKTYLAQTLARIIDVP 140
L GP G GKT LA +AR D P
Sbjct: 26 LRGPAGTGKTTLAMHVARKRDRP 48
>gnl|CDD|183232 PRK11615, PRK11615, hypothetical protein; Provisional.
Length = 185
Score = 33.6 bits (77), Expect = 0.091
Identities = 28/95 (29%), Positives = 47/95 (49%), Gaps = 11/95 (11%)
Query: 185 DEVDKISRKSDNPSITRDVSGEGVQQALLKIM-EGTIASVPPQGGRKHPQQEF----LQV 239
D+ K+ +++N + D +G Q+A++ I+ + T + R QQ LQV
Sbjct: 60 DQSGKLGTQANNMHVYADATG---QKAVIVILGDDTNEDLAVLAKRLEDQQRSRDPQLQV 116
Query: 240 DTTNILFICGGAFAGLDRIISARGEKASIGFSAVV 274
T + + G LD IISA+G+ A +S+VV
Sbjct: 117 VTNKAIELKGHKLQQLDSIISAKGQTA---YSSVV 148
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 33.8 bits (78), Expect = 0.092
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 76 DEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLAR 135
E ++GQ +A++ V V + K +A +L+ GP G GKT LA +++
Sbjct: 23 SEGLVGQEKAREAAGVIV-----EMIKEGK-----IAGRAVLIAGPPGTGKTALAIAISK 72
Query: 136 II--DVPFTM 143
+ D PF
Sbjct: 73 ELGEDTPFCP 82
>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 = 33.7 bits (77), Expect = 0.11
Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 7/74 (9%)
Query: 118 LVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGE------DVENIILKLLQAAD 171
++G GK+ L LA + + A E G+ D I L + D
Sbjct: 167 ILGGESTGKSTLVNKLAAVFNTTSAWEYAREYVEEKLGGDEALQYSDYAQIALGQQRYID 226
Query: 172 YNVERAQRGIVYID 185
Y V A + I +ID
Sbjct: 227 YAVRHAHK-IAFID 239
>gnl|CDD|184586 PRK14240, PRK14240, phosphate transporter ATP-binding protein;
Provisional.
Length = 250
Score = 33.5 bits (77), Expect = 0.11
Identities = 13/39 (33%), Positives = 26/39 (66%), Gaps = 1/39 (2%)
Query: 102 HSSKSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIIDV 139
+ K N+++ ++ + L+GP+GCGK+ +TL R+ D+
Sbjct: 17 QALKKINLDIEENQVTALIGPSGCGKSTFLRTLNRMNDL 55
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 33.5 bits (77), Expect = 0.12
Identities = 17/35 (48%), Positives = 21/35 (60%), Gaps = 5/35 (14%)
Query: 115 NILLVGPTGCGKTYLAQTLARI-----IDVPFTMA 144
NI+L+GP+G GKT+LA L I V FT A
Sbjct: 104 NIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTA 138
>gnl|CDD|178887 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 33.2 bits (77), Expect = 0.12
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 111 LAKSNILLVGPTGCGKTYLAQTLARIIDVPF 141
L NI+L+G G GK+ + + LA+ + F
Sbjct: 2 LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDF 32
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 33.0 bits (76), Expect = 0.14
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 114 SNILLVGPTGCGKTYLAQTL 133
I+L+G +GCGKT L Q L
Sbjct: 2 KKIMLIGRSGCGKTTLTQAL 21
>gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 33.0 bits (76), Expect = 0.14
Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 14/84 (16%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVP-FTM--ADATTLTEAGYVGEDVENIILKLLQAADY 172
+LL GP G GKT LA LA + +D T + +E + + AA
Sbjct: 42 LLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTA-------DVIERVAGE---AATS 91
Query: 173 N-VERAQRGIVYIDEVDKISRKSD 195
+ A+R ++ +DEVD I D
Sbjct: 92 GSLFGARRKLILLDEVDGIHGNED 115
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 32.8 bits (75), Expect = 0.17
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVE 175
++L GP G GKT LA+ +A F + L + Y+G+ ++ +L + A+ N
Sbjct: 220 VILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQK-YLGDG-PKLVRELFRVAEENAP 277
Query: 176 RAQRGIVYIDEVDKISRK 193
IV+IDE+D I K
Sbjct: 278 ----SIVFIDEIDAIGTK 291
>gnl|CDD|163076 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6 family
in eukaryotes. Several members may be found in genome
and interact with each other.
Length = 365
Score = 32.6 bits (75), Expect = 0.18
Identities = 25/108 (23%), Positives = 38/108 (35%), Gaps = 28/108 (25%)
Query: 114 SNILLVGPTGCGKT----YLAQTLARII---DVPFTMA-----DATTLT--------EAG 153
SN+ + G TG GKT Y+ + L DV TL +
Sbjct: 41 SNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLR 100
Query: 154 YVGEDV------ENIILKLLQAADYNVERAQRGIVYIDEVDKISRKSD 195
GE+V + + + L ER I+ +DE+D + D
Sbjct: 101 GSGEEVPTTGLSTSEVFRRL--YKELNERGDSLIIVLDEIDYLVGDDD 146
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 32.6 bits (74), Expect = 0.19
Identities = 29/109 (26%), Positives = 44/109 (40%), Gaps = 23/109 (21%)
Query: 30 LIAGPTVFICDECVELCMDIIREENKSSITKSHEGIPNPQEILRVLDEYVIGQGQAKKVL 89
LI G I D +C + E K ++ + + + L + VIGQ Q K+ L
Sbjct: 148 LINGEGCLIADHLQAVCAFL---EGKHALERPKPTDAVSRALQHDLSD-VIGQEQGKRGL 203
Query: 90 AV-AVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLARII 137
+ A H N+LL+GP G GKT LA + ++
Sbjct: 204 EITAAGGH------------------NLLLIGPPGTGKTMLASRINGLL 234
>gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 32.7 bits (75), Expect = 0.19
Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 24/82 (29%)
Query: 114 SNILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYN 173
+++L GP G GKT LA+ +A F+ +A AG +K L+A
Sbjct: 53 GSLILYGPPGVGKTTLARIIANHTRAHFSSLNAVL---AG----------VKDLRAE--- 96
Query: 174 VERAQ--------RGIVYIDEV 187
V+RA+ R I++IDEV
Sbjct: 97 VDRAKERLERHGKRTILFIDEV 118
>gnl|CDD|183313 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 32.5 bits (75), Expect = 0.21
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 116 ILLVGPTGCGKTYLAQTLAR 135
++L G TG GKT L Q LA
Sbjct: 144 VVLGGNTGSGKTELLQALAN 163
>gnl|CDD|184584 PRK14238, PRK14238, phosphate transporter ATP-binding protein;
Provisional.
Length = 271
Score = 32.5 bits (74), Expect = 0.21
Identities = 14/41 (34%), Positives = 30/41 (73%), Gaps = 2/41 (4%)
Query: 102 HSSKSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIID-VP 140
H+ K+ N+++ ++ + ++GP+GCGK+ +TL R+++ VP
Sbjct: 38 HALKNINLDIHENEVTAIIGPSGCGKSTYIKTLNRMVELVP 78
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 32.5 bits (75), Expect = 0.22
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPF 141
+LL G G KT LA+TLAR + + F
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDF 27
>gnl|CDD|163196 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC transporter,
ATP-binding protein. This ABC transporter ATP-binding
protein is found in a number of genomes in operon-like
contexts strongly suggesting a substrate specificity for
2-aminoethylphosphonate (2-AEP). The characterized
PhnSTUV system is absent in the genomes in which this
system is found. These genomes encode systems for the
catabolism of 2-AEP, making the need for a
2-AEP-specific transporter likely.
Length = 353
Score = 32.3 bits (74), Expect = 0.23
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 7/49 (14%)
Query: 92 AVHNHYKRLAHSSKSSNVELAKSN---ILLVGPTGCGKTYLAQTLARII 137
++ N KR + ++ L+ + L+GP+GCGKT TL RII
Sbjct: 6 SIDNIRKRFGAFTALKDISLSVKKGEFVCLLGPSGCGKT----TLLRII 50
>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 32.3 bits (74), Expect = 0.26
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 118 LVGPTGCGKTYLAQTLARI 136
L+GP GCGK+ L + AR+
Sbjct: 33 LIGPNGCGKSTLLKCFARL 51
>gnl|CDD|183003 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 32.1 bits (74), Expect = 0.30
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 116 ILLVGPTGCGKTYLAQTLAR 135
+ L+G TGCGK+ L Q L R
Sbjct: 369 VALLGRTGCGKSTLLQLLTR 388
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 31.6 bits (71), Expect = 0.35
Identities = 13/25 (52%), Positives = 19/25 (76%)
Query: 113 KSNILLVGPTGCGKTYLAQTLARII 137
K NI+L GP G GKT++A+ LA ++
Sbjct: 194 KKNIILQGPPGVGKTFVARRLAYLL 218
>gnl|CDD|163222 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system.
Length = 852
Score = 31.5 bits (72), Expect = 0.41
Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 12/84 (14%)
Query: 301 PEFIGRLPVLATLEDLDENSLIRI----LSEPKNALIKQYQCLFDMEDVELVFHEDALRE 356
P F+GR+ V+ L LD++ L I L L + + ELV+ E +
Sbjct: 753 PAFLGRMTVIPYLP-LDDDVLAAIVRLKLDRIARRLKENHG-------AELVYSEALVEH 804
Query: 357 IARCAIAHKTGARGLRSILEKILL 380
I ++GAR + +IL + LL
Sbjct: 805 IVARCTEVESGARNIDAILNQTLL 828
Score = 31.1 bits (71), Expect = 0.57
Identities = 23/60 (38%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 75 LDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLA 134
L E VIGQ A + +A + L K V LLVGP+G GKT A LA
Sbjct: 564 LAERVIGQDHALEAIAERIRTARAGLEDPRKPLGV------FLLVGPSGVGKTETALALA 617
>gnl|CDD|172743 PRK14255, PRK14255, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 252
Score = 31.5 bits (71), Expect = 0.42
Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 84 QAKKVLAVA-VHNHYKRLAHSSKSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIIDVPF 141
+AKK++ + VH Y + + K +++ ++ I L+GP+GCGK+ +TL R+ D+
Sbjct: 1 EAKKIITSSDVHLFYGKF-EALKGIDLDFNQNEITALIGPSGCGKSTYLRTLNRMNDL-- 57
Query: 142 TMADATTLTEAGYVGEDV 159
+ T G+++
Sbjct: 58 -IPGVTITGNVSLRGQNI 74
>gnl|CDD|130045 TIGR00972, 3a0107s01c2, phosphate ABC transporter, ATP-binding
protein. This model represents the ATP-binding protein
of a family of ABC transporters for inorganic phosphate.
In the model species Escherichia coli, a constitutive
transporter for inorganic phosphate, with low affinity,
is also present. The high affinity transporter that
includes this polypeptide is induced when extracellular
phosphate concentrations are low. The proteins most
similar to the members of this family but not included
appear to be amino acid transporters.
Length = 247
Score = 31.5 bits (72), Expect = 0.43
Identities = 14/35 (40%), Positives = 26/35 (74%), Gaps = 1/35 (2%)
Query: 105 KSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIID 138
K+ N+++ K+ + L+GP+GCGK+ L ++L R+ D
Sbjct: 18 KNINLDIPKNQVTALIGPSGCGKSTLLRSLNRMND 52
>gnl|CDD|163066 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC.
Length = 615
Score = 31.3 bits (71), Expect = 0.44
Identities = 28/109 (25%), Positives = 41/109 (37%), Gaps = 38/109 (34%)
Query: 55 KSSITKSHEGIPNPQEILRVLDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKS 114
K + KS + + P+ ++GQ +A K L V + + +
Sbjct: 137 KKKLHKSAQSLLRPRAF-----SEIVGQERAIKALLAKVASPFPQ--------------- 176
Query: 115 NILLVGPTGCGKTYLAQTLARII--------------DVPFTMADATTL 149
+I+L GP G GKT T AR+ D PF D TTL
Sbjct: 177 HIILYGPPGVGKT----TAARLALEEAKKLKHTPFAEDAPFVEVDGTTL 221
>gnl|CDD|183258 PRK11650, ugpC, glycerol-3-phosphate transporter ATP-binding
subunit; Provisional.
Length = 356
Score = 31.4 bits (72), Expect = 0.46
Identities = 12/22 (54%), Positives = 17/22 (77%), Gaps = 4/22 (18%)
Query: 116 ILLVGPTGCGKTYLAQTLARII 137
I+LVGP+GCGK+ TL R++
Sbjct: 33 IVLVGPSGCGKS----TLLRMV 50
>gnl|CDD|172761 PRK14273, PRK14273, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 254
Score = 31.2 bits (70), Expect = 0.47
Identities = 14/33 (42%), Positives = 25/33 (75%), Gaps = 1/33 (3%)
Query: 108 NVELAKSNIL-LVGPTGCGKTYLAQTLARIIDV 139
N+++ K++I L+GP+GCGK+ +TL R+ D+
Sbjct: 27 NIKILKNSITALIGPSGCGKSTFLRTLNRMNDL 59
>gnl|CDD|172760 PRK14272, PRK14272, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 252
Score = 31.1 bits (70), Expect = 0.48
Identities = 12/39 (30%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 102 HSSKSSNVELAKSNI-LLVGPTGCGKTYLAQTLARIIDV 139
+ K+ N+++ + + L+GP+GCGKT + + R+ D+
Sbjct: 18 QAVKNVNLDVQRGTVNALIGPSGCGKTTFLRAINRMHDL 56
>gnl|CDD|184411 PRK13946, PRK13946, shikimate kinase; Provisional.
Length = 184
Score = 31.4 bits (72), Expect = 0.49
Identities = 14/35 (40%), Positives = 22/35 (62%)
Query: 111 LAKSNILLVGPTGCGKTYLAQTLARIIDVPFTMAD 145
L K ++LVG G GK+ + + LA ++ +PF AD
Sbjct: 8 LGKRTVVLVGLMGAGKSTVGRRLATMLGLPFLDAD 42
>gnl|CDD|179638 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 31.1 bits (71), Expect = 0.52
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMAD 145
+ LVG GCGKT + LA+ + F D
Sbjct: 5 LFLVGARGCGKTTVGMALAQALGYRFVDTD 34
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 31.0 bits (70), Expect = 0.55
Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 19/74 (25%)
Query: 69 QEILRVLDEY---VIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSN-----ILLVG 120
+++LR+ E VIGQ +A + AV N +R S L+ N L +G
Sbjct: 557 EKLLRMEQELHHRVIGQNEAVE----AVSNAIRR-------SRAGLSDPNRPIGSFLFLG 605
Query: 121 PTGCGKTYLAQTLA 134
PTG GKT L + LA
Sbjct: 606 PTGVGKTELCKALA 619
>gnl|CDD|172741 PRK14253, PRK14253, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 249
Score = 31.0 bits (70), Expect = 0.56
Identities = 15/39 (38%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 102 HSSKSSNVEL-AKSNILLVGPTGCGKTYLAQTLARIIDV 139
+ KS N+ + A+ L+GP+GCGK+ L + L R+ D+
Sbjct: 17 QALKSINLPIPARQVTALIGPSGCGKSTLLRCLNRMNDL 55
>gnl|CDD|131581 TIGR02529, EutJ, ethanolamine utilization protein EutJ family
protein.
Length = 239
Score = 30.9 bits (70), Expect = 0.58
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 273 VVKDSDNRPVGEVLRNLESEDLVKFGLIPEFIGRLPVLATLEDLDENSLIRILSE 327
VV D D +PV V ++ D+V+ G++ +F+G + ++ L+D E L L+
Sbjct: 12 VVLDEDGQPVAGV---MQFADVVRDGIVVDFLGAVEIVRRLKDTLEQKLGIELTH 63
>gnl|CDD|172751 PRK14263, PRK14263, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 261
Score = 31.1 bits (70), Expect = 0.59
Identities = 13/36 (36%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 105 KSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIIDV 139
+ S+V + K+ I +GP+GCGK+ + ++L R+ D+
Sbjct: 25 RDSHVPIRKNEITGFIGPSGCGKSTVLRSLNRMNDL 60
>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 = 30.9 bits (70), Expect = 0.59
Identities = 17/27 (62%), Positives = 19/27 (70%), Gaps = 1/27 (3%)
Query: 111 LAKSNILLVGPTGCGKTYLAQT-LARI 136
LA+ NIL+VG TG GKT LA LA I
Sbjct: 130 LARKNILVVGGTGSGKTTLANALLAEI 156
>gnl|CDD|162839 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis.
Length = 355
Score = 31.0 bits (71), Expect = 0.62
Identities = 20/59 (33%), Positives = 26/59 (44%), Gaps = 18/59 (30%)
Query: 79 VIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLARII 137
VIGQ + L A+ N R+AH+ L GP G GKT ++ARI
Sbjct: 16 VIGQEHIVQTLKNAIKN--GRIAHA------------YLFSGPRGTGKT----SIARIF 56
>gnl|CDD|180719 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 31.0 bits (71), Expect = 0.65
Identities = 11/27 (40%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 113 KSNILLVGPTGCGKTYLAQTLAR-IID 138
N+L G TG GKT+L+ +A+ ++D
Sbjct: 183 NENLLFYGNTGTGKTFLSNCIAKELLD 209
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University).
Length = 637
Score = 30.7 bits (69), Expect = 0.67
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 91 VAVH-NHYKRLAHSSKSSNVELAKSNILLV-GPTGCGKTYLAQTLARII 137
+AVH + + K+ +E A ILL+ GP+GCGK+ + L++ +
Sbjct: 86 LAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKEL 134
>gnl|CDD|180989 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated.
Length = 365
Score = 30.8 bits (70), Expect = 0.69
Identities = 22/73 (30%), Positives = 30/73 (41%), Gaps = 19/73 (26%)
Query: 63 EGIPNPQEILRVLDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPT 122
EG P+P+E + G A+ L A + RL H+ L+ GP
Sbjct: 10 EGAPHPRETTAL-----FGHAAAEAALLDAYRSG--RLHHA------------WLIGGPQ 50
Query: 123 GCGKTYLAQTLAR 135
G GK LA +AR
Sbjct: 51 GIGKATLAYRMAR 63
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme ethanolamine
ammonia lyase. The function of this gene is unknown,
although the presence of an N-terminal GxxGxGK motif
implies a GTP-binding site.
Length = 142
Score = 30.9 bits (70), Expect = 0.69
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 116 ILLVGPTGCGKTYLAQTL 133
I+ +G GCGKT L Q L
Sbjct: 3 IMFIGSVGCGKTTLTQAL 20
>gnl|CDD|184916 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 584
Score = 30.6 bits (69), Expect = 0.70
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 14/57 (24%)
Query: 79 VIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLAR 135
V+GQ + L+ A+ R+ H+ L GP GCGKT A+ LAR
Sbjct: 15 VVGQEHVTEPLSSALDAG--RINHA------------YLFSGPRGCGKTSSARILAR 57
>gnl|CDD|184589 PRK14248, PRK14248, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 268
Score = 30.7 bits (69), Expect = 0.73
Identities = 19/96 (19%), Positives = 45/96 (46%), Gaps = 2/96 (2%)
Query: 70 EILRVLDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNIL-LVGPTGCGKTY 128
+++R E + +L V + Y + ++++ K + L+GP+GCGK+
Sbjct: 3 QMVREKIEIAPFPEAKEHILEVKDLSIYYGEKRAVNDISMDIEKHAVTALIGPSGCGKST 62
Query: 129 LAQTLARIID-VPFTMADATTLTEAGYVGEDVENII 163
+++ R+ D +P ++ L E + + N++
Sbjct: 63 FLRSINRMNDLIPSARSEGEILYEGLNILDSNINVV 98
>gnl|CDD|184314 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 30.6 bits (70), Expect = 0.88
Identities = 18/41 (43%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 115 NILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYV 155
N+L+ PTG GKT LA LA IID F + L + Y
Sbjct: 49 NVLISSPTGSGKT-LAAFLA-IIDELFRLGREGELEDKVYC 87
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 30.5 bits (69), Expect = 0.93
Identities = 30/103 (29%), Positives = 41/103 (39%), Gaps = 14/103 (13%)
Query: 115 NILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNV 174
N++L GP G GKT LA + P L + G DV +K+ +
Sbjct: 36 NLILSGPPGTGKTTSILALAHELLGPNYKEAVLELNASDDRGIDVVRNKIKMFAQKKVTL 95
Query: 175 ERAQRGIVYIDEVDKISRKSDNPSITRDVSGEGVQQALLKIME 217
+ IV +DE D S+T G QQAL + ME
Sbjct: 96 PPGRHKIVILDEAD---------SMT-----SGAQQALRRTME 124
>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 = 30.2 bits (68), Expect = 0.95
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 112 AKSNILLVGPTGCGKTYLAQTLARIID 138
A + +VGPTG GKT L L R+ D
Sbjct: 360 AGQTVAIVGPTGAGKTTLINLLQRVYD 386
>gnl|CDD|162351 TIGR01420, pilT_fam, pilus retraction protein PilT. This model
represents the PilT subfamily of proteins related to
GspE, a protein involved in type II secretion (also
called the General Secretion Pathway). PilT is an
apparent cytosolic ATPase associated with type IV pilus
systems. It is not required for pilin biogenesis, but is
required for twitching motility and social gliding
behaviors, shown in some species, powered by pilus
retraction. Members of this family may be found in some
species that type IV pili but have related structures
for DNA uptake and natural transformation.
Length = 343
Score = 30.4 bits (69), Expect = 0.99
Identities = 13/23 (56%), Positives = 16/23 (69%), Gaps = 3/23 (13%)
Query: 116 ILLVGPTGCGKTYLAQTLARIID 138
IL+ GPTG GK+ TLA +ID
Sbjct: 125 ILVTGPTGSGKS---TTLASMID 144
>gnl|CDD|182336 PRK10253, PRK10253, iron-enterobactin transporter ATP-binding
protein; Provisional.
Length = 265
Score = 30.3 bits (68), Expect = 1.0
Identities = 10/20 (50%), Positives = 17/20 (85%)
Query: 118 LVGPTGCGKTYLAQTLARII 137
++GP GCGK+ L +TL+R++
Sbjct: 38 IIGPNGCGKSTLLRTLSRLM 57
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 30.3 bits (68), Expect = 1.0
Identities = 30/94 (31%), Positives = 42/94 (44%), Gaps = 15/94 (15%)
Query: 107 SNVELAKSNIL-LVGPTGCGKTYLAQTLARIIDVPFT-MADATTLTEA-------GYVGE 157
S V K IL LVGP G GKT L Q++A+ + MA EA Y+G
Sbjct: 342 SRVNKIKGPILCLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRTYIGS 401
Query: 158 DVENIILKLLQAADYNVERAQRGIVYIDEVDKIS 191
+I K+ + N + +DE+DK+S
Sbjct: 402 MPGKLIQKMAKVGVKN------PLFLLDEIDKMS 429
>gnl|CDD|184917 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 30.2 bits (68), Expect = 1.0
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 14/60 (23%)
Query: 79 VIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLARIID 138
VIGQ ++L AV +R++H+ + GP G GKT +A+ LA++++
Sbjct: 18 VIGQEIVVRILKNAVK--LQRVSHA------------YIFAGPRGTGKTTIARILAKVLN 63
>gnl|CDD|162997 TIGR02746, TraC-F-type, type-IV secretion system protein TraC. The
protein family described here is common among the F, P
and I-like type IV secretion systems. Gene symbols
include TraC (F-type), TrbE/VirB4 (P-type) and TraU
(I-type). The protein conyains the Walker A and B motifs
and so is a putative nucleotide triphosphatase.
Length = 797
Score = 30.0 bits (68), Expect = 1.1
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 10/35 (28%)
Query: 115 NILLVGPTGCGKTYLAQTLA----------RIIDV 139
NI +VG +G GK++ Q L +IDV
Sbjct: 432 NIAVVGGSGAGKSFFMQELIVDNLSRGGKVWVIDV 466
>gnl|CDD|184596 PRK14267, PRK14267, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 253
Score = 30.2 bits (68), Expect = 1.1
Identities = 12/39 (30%), Positives = 27/39 (69%), Gaps = 1/39 (2%)
Query: 102 HSSKSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIIDV 139
H K ++++ ++ + L+GP+GCGK+ L +T R++++
Sbjct: 18 HVIKGVDLKIPQNGVFALMGPSGCGKSTLLRTFNRLLEL 56
>gnl|CDD|181256 PRK08154, PRK08154, anaerobic benzoate catabolism transcriptional
regulator; Reviewed.
Length = 309
Score = 29.9 bits (68), Expect = 1.2
Identities = 13/43 (30%), Positives = 20/43 (46%)
Query: 99 RLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLARIIDVPF 141
L+ + + I L+G G GK+ L + LA + VPF
Sbjct: 119 ALSGMLGAGRRAARRRRIALIGLRGAGKSTLGRMLAARLGVPF 161
>gnl|CDD|178433 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 29.8 bits (67), Expect = 1.3
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 98 KRLAHSSKSSNVELAKSN----ILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAG 153
+ A ++ S +K+ I++ GPTG GK+ LA LA+ ++ AD+ +
Sbjct: 2 RFCAATTALSGSGASKTKKEKVIVISGPTGAGKSRLALELAKRLNGEIISADSVQV---- 57
Query: 154 YVGEDV 159
Y G DV
Sbjct: 58 YRGLDV 63
>gnl|CDD|162242 TIGR01187, potA, spermidine/putrescine ABC transporter ATP-binding
subunit. This model describes spermidine/putrescine ABC
transporter, ATP binding subunit in bacteria and its
equivalents in archaea. This transport system belong to
the larger ATP-Binding Cassette (ABC) transporter
superfamily. The characteristic feature of these
transporter is the obligatory coupling of ATP hydrolysis
to substrate translocation. The minimal configuration of
bacterial ABC transport system: an ATPase or ATP binding
subunit; An integral membrane protein; a hydrophilic
polypetpide, which likely functions as substrate binding
protein. Polyamines like spermidine and putrescine play
vital role in cell proliferation, differentiation, and
ion homeostasis. The concentration of polyamines within
the cell are regulated by biosynthesis, degradation and
transport (uptake and efflux included).
Length = 325
Score = 29.8 bits (67), Expect = 1.3
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 118 LVGPTGCGKTYLAQTLARIIDVPF--TMADATTLTE 151
L+GP+GCGKT L + LA M D +T
Sbjct: 1 LLGPSGCGKTTLLRLLAGFEQPDSGSIMLDGEDVTN 36
>gnl|CDD|163168 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD
gene.
Length = 311
Score = 29.9 bits (68), Expect = 1.4
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 116 ILLVGPTGCGKTYLAQTLAR 135
I+L G TG GKT L LA
Sbjct: 130 IVLGGMTGSGKTELLHALAN 149
>gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF.
Length = 282
Score = 30.0 bits (68), Expect = 1.4
Identities = 13/21 (61%), Positives = 15/21 (71%), Gaps = 3/21 (14%)
Query: 116 ILLVGPTGCGKTYLAQTLARI 136
I LVGPTG GKT TLA++
Sbjct: 197 IALVGPTGVGKT---TTLAKL 214
>gnl|CDD|181106 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 29.6 bits (67), Expect = 1.4
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 120 GPTGCGKTYLAQTLAR 135
GP GCGKT A+ LAR
Sbjct: 44 GPRGCGKTSSARILAR 59
>gnl|CDD|130254 TIGR01186, proV, glycine betaine/L-proline transport ATP binding
subunit. This model describes the glycine
betaine/L-proline ATP binding subunit in bacteria and
its equivalents in archaea. This transport system belong
to the larger ATP-Binding Cassette (ABC) transporter
superfamily. The characteristic feature of these
transporter is the obligatory coupling of ATP hydrolysis
to substrate translocation. The minimal configuration of
bacterial ABC transport system: an ATPase or ATP binding
subunit; An integral membrane protein; a hydrophilic
polypetpide, which likely functions as substrate binding
protein. Functionally, this transport system is involved
in osmoregulation. Under conditions of stress, the
organism recruits these transport system to accumulate
glycine betaine and other solutes which offer
osmo-protection. It has been demonstrated that glycine
betaine uptake is accompanied by symport with sodium
ions. The locus has been named variously as proU or
opuA. A gene library from L.lactis functionally
complements an E.coli proU mutant. The comlementing
locus is similar to a opuA locus in B.sutlis. This
clarifies the differences in nomenclature.
Length = 363
Score = 29.8 bits (67), Expect = 1.4
Identities = 10/35 (28%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 105 KSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIID 138
+++ +AK I ++G +G GK+ + L R+I+
Sbjct: 10 NDADLAIAKGEIFVIMGLSGSGKSTTVRMLNRLIE 44
>gnl|CDD|179921 PRK05057, aroK, shikimate kinase I; Reviewed.
Length = 172
Score = 29.7 bits (67), Expect = 1.6
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 113 KSNILLVGPTGCGKTYLAQTLARIIDVPFTMAD 145
K NI LVGP G GK+ + + LA+ +++ F +D
Sbjct: 4 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSD 36
>gnl|CDD|163043 TIGR02858, spore_III_AA, stage III sporulation protein AA. Members
of this protein are the stage III sporulation protein
AA, encoded by one of several genes in the spoIIIA
locus. It seems that this protein is found in a species
if and only if that species is capable of endospore
formation.
Length = 270
Score = 29.6 bits (67), Expect = 1.6
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 115 NILLVGPTGCGKTYLAQTLARII 137
N L++ P CGKT L + LARI+
Sbjct: 113 NTLIISPPQCGKTTLLRDLARIL 135
>gnl|CDD|162129 TIGR00954, 3a01203, Peroxysomal Fatty Acyl CoA Transporter (FAT)
Family protei.
Length = 659
Score = 29.3 bits (66), Expect = 1.7
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 114 SNILLVGPTGCGKTYLAQTLARI 136
+++L+ GP GCGK+ L + L +
Sbjct: 479 NHLLICGPNGCGKSSLFRILGEL 501
>gnl|CDD|182732 PRK10789, PRK10789, putative multidrug transporter
membrane\ATP-binding components; Provisional.
Length = 569
Score = 29.7 bits (67), Expect = 1.7
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 88 VLAVAVHN-HYKRLAHSS-KSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIIDV 139
L V + Y + H + ++ N L +L + GPTG GK+ L + R DV
Sbjct: 313 ELDVNIRQFTYPQTDHPALENVNFTLKPGQMLGICGPTGSGKSTLLSLIQRHFDV 367
>gnl|CDD|172744 PRK14256, PRK14256, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 252
Score = 29.6 bits (66), Expect = 1.7
Identities = 10/39 (25%), Positives = 28/39 (71%), Gaps = 1/39 (2%)
Query: 102 HSSKSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIIDV 139
H+ K +++ ++++ ++GP+GCGK+ + +++ R+ D+
Sbjct: 18 HAVKDVSMDFPENSVTAIIGPSGCGKSTVLRSINRMHDL 56
>gnl|CDD|182996 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed.
Length = 635
Score = 29.5 bits (67), Expect = 1.8
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 116 ILLVGPTGCGKTYL 129
I L+GP GCGKT L
Sbjct: 348 IALIGPNGCGKTTL 361
>gnl|CDD|183503 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 29.6 bits (67), Expect = 1.8
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 15/61 (24%)
Query: 75 LDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLA 134
L E ++GQ + + RL+ + S N+ ++L+ GP G GKT + LA
Sbjct: 13 LLEDILGQDEVVE-----------RLSRAVDSPNL----PHLLVQGPPGSGKTAAVRALA 57
Query: 135 R 135
R
Sbjct: 58 R 58
>gnl|CDD|172750 PRK14262, PRK14262, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 250
Score = 29.5 bits (66), Expect = 1.8
Identities = 24/104 (23%), Positives = 47/104 (45%), Gaps = 11/104 (10%)
Query: 118 LVGPTGCGKTYLAQTLARIID-VPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVER 176
++GP+GCGKT L +++ R+ D +P + + G+D+ + L D R
Sbjct: 34 IIGPSGCGKTTLLRSINRMNDHIPGFRVEGKIYFK----GQDIYDPQL------DVTEYR 83
Query: 177 AQRGIVYIDEVDKISRKSDNPSITRDVSGEGVQQALLKIMEGTI 220
+ G+V+ DN + + G + L +I+E ++
Sbjct: 84 KKVGMVFQKPTPFPMSIYDNVAFGPRIHGVKSKHKLDRIVEESL 127
>gnl|CDD|172375 PRK13851, PRK13851, type IV secretion system protein VirB11;
Provisional.
Length = 344
Score = 29.1 bits (65), Expect = 2.1
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 116 ILLVGPTGCGKTYLAQTLARII 137
+LL GPTG GKT +++TL I
Sbjct: 165 MLLCGPTGSGKTTMSKTLISAI 186
>gnl|CDD|172457 PRK13951, PRK13951, bifunctional shikimate kinase/3-dehydroquinate
synthase; Provisional.
Length = 488
Score = 29.1 bits (65), Expect = 2.1
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMAD 145
I LVG G GK+ + + ++ ++D+ F D
Sbjct: 3 IFLVGMMGSGKSTIGKRVSEVLDLQFIDMD 32
>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
Provisional.
Length = 588
Score = 29.2 bits (66), Expect = 2.1
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 116 ILLVGPTGCGKTYLAQTLARIID 138
+ +VGPTG GK+ L L R+ D
Sbjct: 364 VAIVGPTGAGKSTLINLLQRVFD 386
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 29.0 bits (66), Expect = 2.2
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 116 ILLVGPTGCGKTYLAQTLAR 135
IL+ G G GK+ AQ LA
Sbjct: 260 ILIAGAPGAGKSTFAQALAE 279
>gnl|CDD|184926 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 29.0 bits (65), Expect = 2.2
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 14/57 (24%)
Query: 79 VIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLAR 135
V+GQ KK++ A+ ++H+ + GP G GKT +A+ LA+
Sbjct: 16 VVGQDHVKKLIINALKK--NSISHA------------YIFAGPRGTGKTTVARILAK 58
>gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 29.1 bits (66), Expect = 2.2
Identities = 12/21 (57%), Positives = 15/21 (71%), Gaps = 3/21 (14%)
Query: 116 ILLVGPTGCGKTYLAQTLARI 136
+ LVGPTG GKT TLA++
Sbjct: 224 VALVGPTGVGKT---TTLAKL 241
>gnl|CDD|184590 PRK14249, PRK14249, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 251
Score = 29.3 bits (65), Expect = 2.2
Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 105 KSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIIDV 139
K+ N++ + I ++GP+GCGK+ L + L R+ D+
Sbjct: 21 KNINMDFPERQITAIIGPSGCGKSTLLRALNRMNDI 56
>gnl|CDD|180615 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 28.9 bits (65), Expect = 2.3
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDV 139
+L+ G +G GKT LA LA
Sbjct: 18 VLIDGRSGSGKTTLAGALAARTGF 41
>gnl|CDD|184594 PRK14264, PRK14264, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 305
Score = 29.0 bits (65), Expect = 2.5
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 73 RVLDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVEL-AKSNILLVGPTGCGKTYLAQ 131
+ DE+ + L+V + Y H+ K ++++ KS L+GP+GCGK+ +
Sbjct: 30 QTRDEWTDYEFDGDAKLSVEDLDVYYGDDHALKGVSMDIPEKSVTALIGPSGCGKSTFLR 89
Query: 132 TLARIID 138
L R+ D
Sbjct: 90 CLNRMND 96
>gnl|CDD|169667 PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated.
Length = 351
Score = 28.8 bits (65), Expect = 2.6
Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 23/87 (26%)
Query: 48 DIIREENKSSITKSHEGIPNPQEILRVLDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSS 107
+++ E + +G+P+P E + + G +A+ LA A +L H+
Sbjct: 3 ELMIPEQHDDL----DGVPSPSE-----NTRLFGHEEAEAFLAQAYRE--GKLHHA---- 47
Query: 108 NVELAKSNILLVGPTGCGKTYLAQTLA 134
+L GP G GK LA LA
Sbjct: 48 --------LLFEGPEGIGKATLAFHLA 66
>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
Length = 169
Score = 28.9 bits (65), Expect = 2.8
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPF 141
I LVG G GKT L + LAR + + F
Sbjct: 4 IFLVGYMGAGKTTLGKALARELGLSF 29
>gnl|CDD|172730 PRK14242, PRK14242, phosphate transporter ATP-binding protein;
Provisional.
Length = 253
Score = 28.6 bits (64), Expect = 2.9
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 118 LVGPTGCGKTYLAQTLARIID-VPFTMADATTLTEAGYVGEDV 159
L+GP+GCGK+ + L R+ D +P + L + GE++
Sbjct: 37 LIGPSGCGKSTFLRCLNRMNDLIPGARVEGEILLD----GENI 75
>gnl|CDD|182106 PRK09841, PRK09841, cryptic autophosphorylating protein tyrosine
kinase Etk; Provisional.
Length = 726
Score = 28.7 bits (64), Expect = 2.9
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 110 ELAKSNILLVGPT-GCGKTYLAQTLARII 137
E + +++ G T GKT+++ TLA +I
Sbjct: 528 ETENNILMITGATPDSGKTFVSSTLAAVI 556
>gnl|CDD|178349 PLN02748, PLN02748, tRNA dimethylallyltransferase.
Length = 468
Score = 28.7 bits (64), Expect = 2.9
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDV 159
++++GPTG GK+ LA LA V AD+ + Y G DV
Sbjct: 25 VVVMGPTGSGKSKLAVDLASHFPVEIINADSMQV----YSGLDV 64
>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 367
Score = 28.7 bits (64), Expect = 2.9
Identities = 23/87 (26%), Positives = 35/87 (40%), Gaps = 4/87 (4%)
Query: 114 SNILLVGPTGCGKTYLAQTLARIIDVPFTMAD----ATTLTEAGYVGEDVENIILKLLQA 169
+L GP G GKT A+ LAR I+ P + + E + + I L+
Sbjct: 40 QALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDDIRNLIDQ 99
Query: 170 ADYNVERAQRGIVYIDEVDKISRKSDN 196
+ + I IDEV +S + N
Sbjct: 100 VRIPPQTGKYKIYIIDEVHMLSSAAFN 126
>gnl|CDD|129727 TIGR00641, acid_CoA_mut_N, methylmalonyl-CoA mutase N-terminal
domain. Methylmalonyl-CoA mutase (EC 5.4.99.2)
catalyzes a reversible isomerization between
L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an
adenosylcobalamin cofactor. It may be a homodimer, as in
mitochondrion, or a heterodimer with partially
homologous beta chain that does not bind the
adenosylcobalamin cofactor, as in Propionibacterium
freudenreichii. The most similar archaeal sequences are
separate chains, such as AF2215 abd AF2219 of
Archaeoglobus fulgidus, that correspond roughly to the
first 500 and last 130 residues, respectively of known
methylmalonyl-CoA mutases. This model describes the
N-terminal domain subfamily. In a neighbor-joining tree,
AF2215 branches with a bacterial isobutyryl-CoA mutase,
which is also the same length. Scoring between the noise
and trusted cutoffs are the non-catalytic, partially
homologous beta chains from certain heterodimeric
examples of 5.4.99.2.
Length = 528
Score = 28.6 bits (64), Expect = 3.0
Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 7/74 (9%)
Query: 152 AGYVGEDVENIILKLLQAADYNVERAQRGI-VYIDEVDKISRKSDNPSITRDVSGEGVQQ 210
AG+ + N + N+ Q+G+ V D SDNP + DV GV
Sbjct: 57 AGFSTAEESNAFYR------RNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAI 110
Query: 211 ALLKIMEGTIASVP 224
++ M +P
Sbjct: 111 DSIEDMRILFDGIP 124
>gnl|CDD|184412 PRK13947, PRK13947, shikimate kinase; Provisional.
Length = 171
Score = 28.5 bits (64), Expect = 3.1
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 115 NILLVGPTGCGKTYLAQTLARIIDVPFTMADA 146
NI+L+G G GKT + + +A + F D
Sbjct: 3 NIVLIGFMGTGKTTVGKRVATTLSFGFIDTDK 34
>gnl|CDD|184587 PRK14241, PRK14241, phosphate transporter ATP-binding protein;
Provisional.
Length = 258
Score = 28.5 bits (64), Expect = 3.4
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 111 LAKSNILLVGPTGCGKTYLAQTLARIIDV 139
+S +GP+GCGK+ + +TL R+ +V
Sbjct: 28 EPRSVTAFIGPSGCGKSTVLRTLNRMHEV 56
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 28.7 bits (64), Expect = 3.4
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 100 LAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLA 134
+AH V K N++ +GP G GKT+LA L
Sbjct: 86 IAHLGTLDFV-TGKENVVFLGPPGTGKTHLAIGLG 119
>gnl|CDD|182817 PRK10895, PRK10895, lipopolysaccharide ABC transporter ATP-binding
protein; Provisional.
Length = 241
Score = 28.3 bits (63), Expect = 3.6
Identities = 24/76 (31%), Positives = 32/76 (42%), Gaps = 17/76 (22%)
Query: 118 LVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVERA 177
L+GP G GKT F M +AG + D E+I L L RA
Sbjct: 34 LLGPNGAGKT-----------TTFYMVVGIVPRDAGNIIIDDEDISLLPLH------ARA 76
Query: 178 QRGIVYIDEVDKISRK 193
+RGI Y+ + I R+
Sbjct: 77 RRGIGYLPQEASIFRR 92
>gnl|CDD|163254 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP.
Length = 226
Score = 28.3 bits (64), Expect = 3.7
Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 21/80 (26%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNV- 174
+ L G +G GK++L Q A G+ + L L AD V
Sbjct: 41 LYLWGESGSGKSHLLQAACA---------------AAEERGKSAIYLPLAELAQADPEVL 85
Query: 175 ---ERAQRGIVYIDEVDKIS 191
E+A +V +D+V+ I+
Sbjct: 86 EGLEQAD--LVCLDDVEAIA 103
>gnl|CDD|131926 TIGR02880, cbbX_cfxQ, probable Rubsico expression protein CbbX.
Proteins in this family are now designated CbbX. Some
previously were CfxQ (carbon fixation Q). Its gene is
often found immmediately downstream of the Rubisco large
and small chain genes, and it is suggested to be
necessary for Rubisco expression. CbbX has been shown to
be necessary for photoautotrophic growth. This protein
belongs to the larger family of pfam00004, ATPase family
Associated with various cellular Activities. Within that
larger family, members of this family are most closely
related to the stage V sporulation protein K, or SpoVK,
in endospore-forming bacteria such as Bacillus subtilis.
Length = 284
Score = 28.3 bits (63), Expect = 3.7
Identities = 39/156 (25%), Positives = 72/156 (46%), Gaps = 21/156 (13%)
Query: 69 QEILRVLDEYVIGQGQAK-KVLAVA----VHNHYKRLAHSSKSSNVELAKSNILLVGPTG 123
E+L LD +IG K ++ +A V +RL +S + + ++ G G
Sbjct: 14 TEVLDQLDRELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMS-----FTGNPG 68
Query: 124 CGKTYLAQTLARII-DVPFT-MADATTLTEAGYVGEDVENIILKLLQAADYNVERAQRGI 181
GKT +A +A+I+ + + ++T VG+ + + K + ++RA G+
Sbjct: 69 TGKTTVALRMAQILHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEI----LKRAMGGV 124
Query: 182 VYIDEVDKISRKSDNPSITRDVSGEGVQQALLKIME 217
++IDE + R P RD E + + LL++ME
Sbjct: 125 LFIDEAYYLYR----PDNERDYGQEAI-EILLQVME 155
>gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein
YbbL; Provisional.
Length = 225
Score = 28.5 bits (64), Expect = 3.7
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 5/43 (11%)
Query: 117 LLVGPTGCGKTYLAQTLARIID-----VPFTMADATTLTEAGY 154
L+ GP+GCGK+ L + +A +I + F D +TL Y
Sbjct: 37 LITGPSGCGKSTLLKIVASLISPTSGTLLFEGEDISTLKPEIY 79
>gnl|CDD|184583 PRK14237, PRK14237, phosphate transporter ATP-binding protein;
Provisional.
Length = 267
Score = 28.1 bits (63), Expect = 4.1
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 5/43 (11%)
Query: 118 LVGPTGCGK-TYLAQTLARIIDVPFTMADATTLTEAGYVGEDV 159
L+GP+G GK TYL ++L R+ D T+ A + Y G D+
Sbjct: 51 LIGPSGSGKSTYL-RSLNRMND---TIDIARVTGQILYRGIDI 89
>gnl|CDD|184581 PRK14235, PRK14235, phosphate transporter ATP-binding protein;
Provisional.
Length = 267
Score = 28.2 bits (63), Expect = 4.2
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 87 KVLAVAVHNHYKRLAHSSKSSNVE-LAKSNILLVGPTGCGKTYLAQTLARIID 138
K+ A V Y + +++ K+ +GP+GCGK+ + L R+ D
Sbjct: 19 KMRARDVSVFYGE-KQALFDVDLDIPEKTVTAFIGPSGCGKSTFLRCLNRMND 70
>gnl|CDD|161731 TIGR00145, TIGR00145, FTR1 family protein. A characterized member
from yeast acts as oxidase-coupled high affinity iron
transporter. Note that the apparent member from E. coli
K12-MG1655 has a frameshift by homology with member
sequences from other species.
Length = 283
Score = 28.2 bits (63), Expect = 4.2
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 227 GGRKHPQQEFLQVDTTNILFICGGAFAG 254
GG + + F + ++ +LFI G G
Sbjct: 174 GGSRLSLKIFFILSSSLLLFIAAGLLGG 201
>gnl|CDD|181868 PRK09452, potA, putrescine/spermidine ABC transporter ATPase
protein; Reviewed.
Length = 375
Score = 28.0 bits (63), Expect = 4.2
Identities = 11/20 (55%), Positives = 15/20 (75%), Gaps = 4/20 (20%)
Query: 118 LVGPTGCGKTYLAQTLARII 137
L+GP+GCGKT T+ R+I
Sbjct: 45 LLGPSGCGKT----TVLRLI 60
>gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding
protein; Provisional.
Length = 369
Score = 28.1 bits (63), Expect = 4.3
Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 5/38 (13%)
Query: 101 AHSSKSSNVELAKSN-ILLVGPTGCGKTYLAQTLARII 137
SK N+++ + ++ VGP+GCGK+ TL R+I
Sbjct: 16 VVISKDINLDIHEGEFVVFVGPSGCGKS----TLLRMI 49
>gnl|CDD|184377 PRK13894, PRK13894, conjugal transfer ATPase TrbB; Provisional.
Length = 319
Score = 28.2 bits (63), Expect = 4.4
Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 20/59 (33%)
Query: 75 LDEYV---IGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLA 130
LD+YV I ++ + AV H NIL++G TG GKT L
Sbjct: 124 LDQYVERGIMTAAQREAIIAAVRAH-----------------RNILVIGGTGSGKTTLV 165
>gnl|CDD|172756 PRK14268, PRK14268, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 258
Score = 28.0 bits (62), Expect = 4.4
Identities = 12/36 (33%), Positives = 26/36 (72%), Gaps = 1/36 (2%)
Query: 105 KSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIIDV 139
K+ ++++ K+++ L+GP+GCGK+ + L R+ D+
Sbjct: 29 KNVSMQIPKNSVTALIGPSGCGKSTFIRCLNRMNDL 64
>gnl|CDD|183993 PRK13354, PRK13354, tyrosyl-tRNA synthetase; Provisional.
Length = 410
Score = 27.9 bits (63), Expect = 4.5
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 9/49 (18%)
Query: 309 VLATLEDLDENSLIRILSEPKNALIKQYQCLFDMEDVELVFHEDALREI 357
L T E + N+ +Q LFD E E+V + D L ++
Sbjct: 90 KLLTDEQVQHNA---------KTYTEQIFKLFDFEKTEIVNNSDWLSKL 129
>gnl|CDD|183084 PRK11308, dppF, dipeptide transporter ATP-binding subunit;
Provisional.
Length = 327
Score = 28.0 bits (63), Expect = 4.6
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 8/41 (19%)
Query: 119 VGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDV 159
VG +GCGK+ TLAR++ TM + T E Y G+D+
Sbjct: 47 VGESGCGKS----TLARLL----TMIETPTGGELYYQGQDL 79
>gnl|CDD|172748 PRK14260, PRK14260, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 259
Score = 28.1 bits (62), Expect = 4.8
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 118 LVGPTGCGKTYLAQTLARI 136
++GP+GCGK+ +TL RI
Sbjct: 38 IIGPSGCGKSTFIKTLNRI 56
>gnl|CDD|179010 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 27.9 bits (63), Expect = 4.8
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 114 SNILLVGPTGCGKT 127
N+L+ GP G GKT
Sbjct: 56 LNVLIYGPPGTGKT 69
>gnl|CDD|183014 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 27.9 bits (63), Expect = 4.9
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 112 AKSNILLVGPTGCGKTYLAQTL 133
A I LVGP+G GKT L L
Sbjct: 375 AGQRIALVGPSGAGKTSLLNAL 396
>gnl|CDD|177412 PHA02583, 11, baseplate wedge subunit and tail pin; Provisional.
Length = 218
Score = 28.1 bits (63), Expect = 5.0
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 8/64 (12%)
Query: 173 NVERAQRGIVY------IDEVDKISRKSDNPSI--TRDVSGEGVQQALLKIMEGTIASVP 224
+++ Q+G+ Y ID++ ++ I T +VS EGVQQ GT+
Sbjct: 39 TIDQLQKGVYYPNVQSAIDDLATLAELPVGGVIITTENVSPEGVQQVETLTFSGTVTDSD 98
Query: 225 PQGG 228
P G
Sbjct: 99 PDGD 102
>gnl|CDD|179223 PRK01109, PRK01109, ATP-dependent DNA ligase; Provisional.
Length = 590
Score = 28.0 bits (63), Expect = 5.0
Identities = 29/94 (30%), Positives = 45/94 (47%), Gaps = 20/94 (21%)
Query: 158 DVENIILKLLQAA----DYNVERAQRGIVYIDEVDKI---SRKSDNPSITR---DVSGEG 207
+ I+ K+ A Y+ ERAQ ++ DK+ SR+ +N IT DV E
Sbjct: 238 SPKEILKKMGGEALVEYKYDGERAQ---IHKKG-DKVKIFSRRLEN--ITHQYPDVV-EY 290
Query: 208 VQQALLK---IMEGTIASVPPQGGRKHPQQEFLQ 238
++A+ I+EG I +V P+ G P QE +
Sbjct: 291 AKEAIKAEEAIVEGEIVAVDPETGEMRPFQELMH 324
>gnl|CDD|172753 PRK14265, PRK14265, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 274
Score = 27.7 bits (61), Expect = 5.5
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 112 AKSNILLVGPTGCGKTYLAQTLARIIDV 139
AK I +GP+GCGK+ L + R+ D+
Sbjct: 45 AKKIIAFIGPSGCGKSTLLRCFNRMNDL 72
>gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit;
Provisional.
Length = 353
Score = 27.7 bits (62), Expect = 5.5
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 4/22 (18%)
Query: 116 ILLVGPTGCGKTYLAQTLARII 137
+ L+GP+G GKT TL RII
Sbjct: 31 VALLGPSGSGKT----TLLRII 48
>gnl|CDD|161743 TIGR00174, miaA, tRNA isopentenyltransferase (miaA). Catalyzes the
first step in the modification of an adenosine near the
anticodon to 2-methylthio-N6-isopentyladenosine.
Length = 287
Score = 27.7 bits (62), Expect = 5.5
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADA 146
I ++GPT GK+ LA LA+ ++ D+
Sbjct: 2 IFIMGPTAVGKSQLAIQLAKKLNAEIISVDS 32
>gnl|CDD|184928 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 491
Score = 27.8 bits (62), Expect = 5.7
Identities = 14/24 (58%), Positives = 16/24 (66%), Gaps = 4/24 (16%)
Query: 114 SNILLVGPTGCGKTYLAQTLARII 137
+ILLVG +G GKT T ARII
Sbjct: 36 QSILLVGASGVGKT----TCARII 55
>gnl|CDD|129208 TIGR00101, ureG, urease accessory protein UreG. This model
represents UreG, a GTP hydrolase that acts in the
assembly of the nickel metallocenter of urease. It is
found only in urease-positive species, although some
urease-positive species (e.g. Bacillus subtilis) lack
this protein. A similar protein, hypB, is an accessory
protein for expression of hydrogenase, which also uses
nickel.
Length = 199
Score = 27.9 bits (62), Expect = 5.8
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVE 160
I + GP G GKT L + L R + + +A +T Y ED E
Sbjct: 4 IGVAGPVGSGKTALIEALTRALRQKYQLA---VITNDIYTQEDAE 45
>gnl|CDD|184357 PRK13873, PRK13873, conjugal transfer ATPase TrbE; Provisional.
Length = 811
Score = 27.6 bits (62), Expect = 5.8
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 117 LLVGPTGCGKTYLAQTLA 134
L+VGPTG GK+ L +A
Sbjct: 445 LVVGPTGAGKSVLLALMA 462
>gnl|CDD|172759 PRK14271, PRK14271, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 276
Score = 27.8 bits (61), Expect = 6.0
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 112 AKSNILLVGPTGCGKTYLAQTLARIID 138
A++ L+GPTG GKT +TL R+ D
Sbjct: 46 ARAVTSLMGPTGSGKTTFLRTLNRMND 72
>gnl|CDD|184585 PRK14239, PRK14239, phosphate transporter ATP-binding protein;
Provisional.
Length = 252
Score = 27.8 bits (62), Expect = 6.1
Identities = 9/22 (40%), Positives = 17/22 (77%)
Query: 118 LVGPTGCGKTYLAQTLARIIDV 139
L+GP+G GK+ L +++ R+ D+
Sbjct: 36 LIGPSGSGKSTLLRSINRMNDL 57
>gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 27.5 bits (61), Expect = 6.1
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 115 NILLVGPTGCGKTYLAQTLA 134
+++L PTG GKT A A
Sbjct: 26 DVILAAPTGSGKTLAALLPA 45
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in this
group and are missing from the Clostridium group.
Length = 261
Score = 27.8 bits (62), Expect = 6.2
Identities = 36/153 (23%), Positives = 68/153 (44%), Gaps = 21/153 (13%)
Query: 71 ILRVLDEYVIGQGQAK---KVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKT 127
+ R L V G + K K + + + KR K+S L +++ G G GKT
Sbjct: 1 VERELSRMV-GLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVL---HMIFKGNPGTGKT 56
Query: 128 YLAQTLARI---IDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVERAQRGIVYI 184
+A+ L ++ ++V + + A VGE + + K + +++A G+++I
Sbjct: 57 TVARILGKLFKEMNV-LSKGHLIEVERADLVGEYIGHTAQKTRE----VIKKALGGVLFI 111
Query: 185 DEVDKISRKSDNPSITRDVSGEGVQQALLKIME 217
DE ++R + +D E + L+K ME
Sbjct: 112 DEAYSLARGGE-----KDFGKEAI-DTLVKGME 138
>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 = 27.7 bits (62), Expect = 6.5
Identities = 23/81 (28%), Positives = 33/81 (40%), Gaps = 19/81 (23%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDV----------PFTMADATTLTE-AGYVGED------ 158
+ LVGP+G GK+ L L +D P ADA + + +V +
Sbjct: 351 VALVGPSGAGKSTLLNLLLGFVDPTEGSIAVNGVPLADADADSWRDQIAWVPQHPFLFAG 410
Query: 159 --VENIILKLLQAADYNVERA 177
ENI L A+D + RA
Sbjct: 411 TIAENIRLARPDASDAEIRRA 431
>gnl|CDD|131085 TIGR02030, BchI-ChlI, magnesium chelatase ATPase subunit I. This
model represents one of two ATPase subunits of the
trimeric magnesium chelatase responsible for insertion
of magnesium ion into protoporphyrin IX. This is an
essential step in the biosynthesis of both chlorophyll
and bacteriochlorophyll. This subunit is found in green
plants, photosynthetic algae, cyanobacteria and other
photosynthetic bacteria.
Length = 337
Score = 27.5 bits (61), Expect = 6.6
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 136 IIDVPFTMAD-ATTLTEAGYVGE-DVENIILKLLQAADYNV-ERAQRGIVYIDEVD 188
II P + D TE G D+E + + ++A + + RA RGI+YIDEV+
Sbjct: 86 IIKKPVPVVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLARANRGILYIDEVN 141
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 27.7 bits (62), Expect = 6.6
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADA 146
I+L+G G GK+ LA+ L +++P DA
Sbjct: 4 IILIGSGGSGKSTLARQLGEKLNIPVHHLDA 34
>gnl|CDD|179771 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 27.5 bits (62), Expect = 6.6
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 120 GPTGCGKTYLAQTLARIIDVPF 141
GP G GKT +A+ LA + +
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKH 28
>gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 27.7 bits (62), Expect = 6.6
Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 17/59 (28%)
Query: 79 VIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLARII 137
VIGQ A +V+ A + +++++G G GK+ LA+ +A ++
Sbjct: 33 VIGQEHAVEVIKKAAKQ-----------------RRHVMMIGSPGTGKSMLAKAMAELL 74
>gnl|CDD|177850 PLN02199, PLN02199, shikimate kinase.
Length = 303
Score = 27.4 bits (60), Expect = 6.8
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 115 NILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGEDVENI 162
++ LVG G GKT + + +++++ +T D TL E G V I
Sbjct: 104 SMYLVGMMGSGKTTVGKLMSKVLG--YTFFDCDTLIEQAMNGTSVAEI 149
>gnl|CDD|184597 PRK14270, PRK14270, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 251
Score = 27.6 bits (61), Expect = 6.9
Identities = 12/33 (36%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 108 NVELAKSNIL-LVGPTGCGKTYLAQTLARIIDV 139
N+ + ++ I L+GP+GCGK+ + L R+ D+
Sbjct: 24 NLPIYENKITALIGPSGCGKSTFLRCLNRMNDL 56
>gnl|CDD|116881 pfam08298, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 358
Score = 27.4 bits (61), Expect = 7.1
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 110 ELAKSNILLVGPTGCGKTYLAQTLARII-DVPF 141
E K + L+GP G GK+ LA+ L +++ VP
Sbjct: 82 EERKQILYLLGPVGGGKSSLAERLKKLLELVPI 114
>gnl|CDD|162298 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
glucokinase family. This model represents a subfamily
of proteins that includes thermoresistant and
thermosensitve isozymes of gluconate kinase
(gluconokinase) in E. coli and other related proteins;
members of this family are often named by similarity to
the thermostable isozyme. These proteins show homology
to shikimate kinases and adenylate kinases but not to
gluconate kinases from the FGGY family of carbohydrate
kinases.
Length = 163
Score = 27.4 bits (61), Expect = 7.2
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMAD 145
+L+G G GK+ +A LA + F D
Sbjct: 1 FVLMGVAGSGKSTIASALAHRLGAKFIEGD 30
>gnl|CDD|114590 pfam05872, DUF853, Bacterial protein of unknown function (DUF853).
This family consists of several bacterial proteins of
unknown function. One member from Brucella melitensis is
thought to be an ATPase.
Length = 504
Score = 27.4 bits (61), Expect = 7.3
Identities = 14/32 (43%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 117 LLVGPTGCGKTYLAQTLAR---IIDVPFTMAD 145
L+ G TG GKT Q LA VP +AD
Sbjct: 25 LIAGATGTGKTVTLQVLAESFSDAGVPVFLAD 56
>gnl|CDD|182342 PRK10261, PRK10261, glutathione transporter ATP-binding protein;
Provisional.
Length = 623
Score = 27.5 bits (61), Expect = 7.7
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 95 NHYKRLAHSSKSSNVELAKSNIL-LVGPTGCGKTYLAQTLARIID 138
N R H+ + + +L L LVG +G GK+ + L R+++
Sbjct: 331 NRVTREVHAVEKVSFDLWPGETLSLVGESGSGKSTTGRALLRLVE 375
>gnl|CDD|181233 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 27.3 bits (61), Expect = 7.7
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 110 ELAKSNI--LLVGPTGCGKTYLAQTLA 134
E+ K N+ LL G G GKTYLA +A
Sbjct: 109 EMKKENVGLLLWGSVGTGKTYLAACIA 135
>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 = 27.4 bits (61), Expect = 7.8
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 116 ILLVGPTGCGKTYLAQTLARIID 138
+ LVGP+G GK+ L Q L R D
Sbjct: 369 VALVGPSGAGKSTLFQLLLRFYD 391
>gnl|CDD|178393 PLN02796, PLN02796, D-glycerate 3-kinase.
Length = 347
Score = 27.4 bits (61), Expect = 8.0
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 117 LLVG---PTGCGKTYLAQTLARIIDV 139
L++G P GCGKT L L + +
Sbjct: 101 LVIGISAPQGCGKTTLVFALVYLFNA 126
>gnl|CDD|172749 PRK14261, PRK14261, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 253
Score = 27.1 bits (60), Expect = 8.1
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 118 LVGPTGCGKTYLAQTLARIIDV 139
L+GP+GCGK+ L + R+ D+
Sbjct: 37 LIGPSGCGKSTLLRCFNRMNDL 58
>gnl|CDD|184430 PRK13975, PRK13975, thymidylate kinase; Provisional.
Length = 196
Score = 27.4 bits (61), Expect = 8.1
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 8/62 (12%)
Query: 116 ILLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYV------GEDVENIILKLLQA 169
I+ G G GKT A+ LA ++ +T T + G + G + L LL A
Sbjct: 5 IVFEGIDGSGKTTQAKLLAEKLNAFWTC--EPTDGKIGKLIREILSGSKCDKETLALLFA 62
Query: 170 AD 171
AD
Sbjct: 63 AD 64
>gnl|CDD|184458 PRK14021, PRK14021, bifunctional shikimate kinase/3-dehydroquinate
synthase; Provisional.
Length = 542
Score = 27.1 bits (60), Expect = 8.2
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 117 LLVGPTGCGKTYLAQTLARIIDVPFTMADATTLTEAG 153
+++G G GKT + + +A+++ +PF AD E G
Sbjct: 10 VIIGMMGAGKTRVGKEVAQMMRLPFADADVEIEREIG 46
>gnl|CDD|185476 PTZ00143, PTZ00143, deoxyuridine 5'-triphosphate
nucleotidohydrolase; Provisional.
Length = 155
Score = 27.4 bits (61), Expect = 8.2
Identities = 23/87 (26%), Positives = 37/87 (42%), Gaps = 14/87 (16%)
Query: 120 GPTGCGKTYLAQTLARIIDVPFTMADATTLTEAGYVGE---------DVENIILK---LL 167
G G ++L + I P +A++ L +AGY GE D I K L+
Sbjct: 62 GSDGKNVSWLLFPRSSISKTPLRLANSIGLIDAGYRGELIAAVDNIKDEPYTIKKGDRLV 121
Query: 168 QAADYNVERAQRGIVYIDEVDKISRKS 194
Q ++ E +V DE+D+ +R
Sbjct: 122 QLVSFDGEPITFELV--DELDETTRGE 146
>gnl|CDD|179068 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 27.0 bits (61), Expect = 8.8
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 63 EGIPNPQEILRVLDE 77
+G +P +ILRVL
Sbjct: 986 DGSIDPHDILRVLGV 1000
>gnl|CDD|148176 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several
bacterial zeta toxin proteins. Zeta toxin is thought to
be part of a postregulational killing system in
bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 27.2 bits (61), Expect = 9.0
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 116 ILLVGPTGCGKTYLA 130
+LL G G GKT LA
Sbjct: 15 VLLGGQPGAGKTELA 29
>gnl|CDD|162908 TIGR02538, type_IV_pilB, type IV-A pilus assembly ATPase PilB.
This model describes a protein of type IV pilus
biogenesis designated PilB in Pseudomonas aeruginosa but
PilF in Neisseria gonorrhoeae; the more common usage,
reflected here, is PilB. This protein is an ATPase
involved in protein export for pilin assembly and is
closely related to GspE (TIGR02533) of type II
secretion, also called the main terminal branch of the
general secretion pathway. Note that type IV pilus
systems are often divided into type IV-A and IV-B, with
the latter group including bundle-forming pilus,
mannose-sensitive hemagglutinin, etc. Members of this
family are found in type IV-A systems.
Length = 564
Score = 26.9 bits (60), Expect = 9.1
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 26 EVRKLI--AGPTVFICDECVELCMDIIREENKSSITKSHEGIPNPQEILRV 74
E+ +LI G + I + + M +R S + K +G+ + +E+LRV
Sbjct: 514 EIAELILKGGNALQIAELAQKEGMRTLRR---SGLLKVKQGVTSLEEVLRV 561
>gnl|CDD|163508 TIGR03796, NHPM_micro_ABC1, NHPM bacteriocin system ABC
transporter, peptidase/ATP-binding protein. This
protein describes an multidomain ABC transporter subunit
that is one of three protein families associated with
some regularity with a distinctive family of putative
bacteriocins. It includes a bacteriocin-processing
peptidase domain at the N-terminus. Model TIGR03793
describes a conserved propeptide region for this
bacteriocin family, unusual because it shows obvious
homology a region of the enzyme nitrile hydratase up to
the classic Gly-Gly cleavage motif. This family is
therefore predicted to be a subunit of a bacteriocin
processing and export system characteristic to this
system that we designate NHPM, Nitrile Hydratase
Propeptide Microcin.
Length = 710
Score = 26.8 bits (60), Expect = 9.6
Identities = 8/24 (33%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 114 SNILLVGPTGCGKTYLAQTLARII 137
+ LVG +G GK+ T+A+++
Sbjct: 506 QRVALVGGSGSGKS----TIAKLV 525
>gnl|CDD|172739 PRK14251, PRK14251, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 251
Score = 26.9 bits (59), Expect = 9.6
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 118 LVGPTGCGKTYLAQTLARIID 138
L+GP+GCGK+ + L R+ D
Sbjct: 35 LIGPSGCGKSTFLRCLNRMND 55
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 27.1 bits (60), Expect = 9.7
Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 14/56 (25%)
Query: 79 VIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLA 134
V+GQ K+VL A+ RL H+ L GP G GKT A+ +A
Sbjct: 16 VVGQEHVKEVLLAALRQ--GRLGHA------------YLFSGPRGVGKTTTARLIA 57
>gnl|CDD|180175 PRK05632, PRK05632, phosphate acetyltransferase; Reviewed.
Length = 684
Score = 27.0 bits (61), Expect = 9.7
Identities = 19/73 (26%), Positives = 28/73 (38%), Gaps = 15/73 (20%)
Query: 114 SNILLVGP-TGCGKTY----LAQTLAR----------IIDVPFTMADATTLTEAGYVGED 158
+I L TG G T L + L R I P TM++ L +G + E
Sbjct: 3 RSIYLAPTGTGVGLTSVSLGLMRALERKGVKVGFFKPIAQPPLTMSEVEALLASGQLDEL 62
Query: 159 VENIILKLLQAAD 171
+E I+ + A
Sbjct: 63 LEEIVARYHALAK 75
>gnl|CDD|172747 PRK14259, PRK14259, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 269
Score = 27.1 bits (60), Expect = 9.7
Identities = 10/22 (45%), Positives = 18/22 (81%)
Query: 118 LVGPTGCGKTYLAQTLARIIDV 139
L+GP+GCGK+ + ++L R+ D+
Sbjct: 44 LIGPSGCGKSTVLRSLNRMNDL 65
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 26.8 bits (59), Expect = 9.8
Identities = 13/24 (54%), Positives = 18/24 (75%), Gaps = 1/24 (4%)
Query: 111 LAK-SNILLVGPTGCGKTYLAQTL 133
LAK +N+LL GP G GK++LA +
Sbjct: 103 LAKGANLLLFGPPGGGKSHLAAAI 126
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 0.135 0.380
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 6,758,358
Number of extensions: 446755
Number of successful extensions: 1429
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1395
Number of HSP's successfully gapped: 225
Length of query: 424
Length of database: 5,994,473
Length adjustment: 96
Effective length of query: 328
Effective length of database: 3,920,105
Effective search space: 1285794440
Effective search space used: 1285794440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.1 bits)