RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14062
(388 letters)
>gnl|CDD|213241 cd03274, ABC_SMC4_euk, ATP-binding cassette domain of eukaryotic
SMC4 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 212
Score = 142 bits (361), Expect = 1e-40
Identities = 75/214 (35%), Positives = 91/214 (42%), Gaps = 100/214 (46%)
Query: 75 LIITKIVAFNFKSYAGYVTLGPFNTGEVEQISMMPPKGKTEKETGLLEYLEEIIGTNRYK 134
LIITK+V NFKSYAG +GPF +K
Sbjct: 1 LIITKLVLENFKSYAGEQVIGPF-----------------------------------HK 25
Query: 135 RFNAIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGKSNVIDSMLFVFGYRASKIRANKLSV 194
F +AI+GPNGSGKSNVIDSMLFVFG+RASK+R KLS
Sbjct: 26 SF----------------------SAIVGPNGSGKSNVIDSMLFVFGFRASKMRQKKLSD 63
Query: 195 LMHKSDQVGGVSRCSVAIHFAQIIDKPNEEYEIIPGTDLEIARTAFYDNSSYYTLNGKKV 254
L+H S + CSV +HF +IIDKP
Sbjct: 64 LIHNSAGHPNLDSCSVEVHFQEIIDKP--------------------------------- 90
Query: 255 HFKEVAKVLRDHGVDLLNNRFLILQ---EPIAKM 285
+L+ G+DL +NRFLILQ E IA+M
Sbjct: 91 -------LLKSKGIDLDHNRFLILQGEVEQIAQM 117
Score = 29.2 bits (66), Expect = 2.8
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 100 GEVEQISMMPPK 111
GEVEQI+ MP K
Sbjct: 109 GEVEQIAQMPKK 120
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 136 bits (344), Expect = 6e-35
Identities = 73/268 (27%), Positives = 119/268 (44%), Gaps = 41/268 (15%)
Query: 157 RFNAIIGPNGSGKSNVIDSMLFVFGYRASK-IRANKLSVLMHKSDQVGGVSRCSVAIHFA 215
F AI+GPNGSGKSN++D++LFV G R++K +R+ +LS L+H S V+ V I F
Sbjct: 24 GFTAIVGPNGSGKSNILDAILFVLGERSAKSLRSERLSDLIHYSKSGAFVNSAEVTITF- 82
Query: 216 QIIDKPNEEYEIIPGTDLEIARTAFYDNSSYYTLNGKKVHFKEVAKVLRDHGVDLLNNRF 275
D + + I ++ I R + S Y +NGK V K+VA++L G+ F
Sbjct: 83 ---DNED-KELPIDDPEVSIRRRVYRGGDSEYYINGKDVTKKDVAELLESAGISPEAYNF 138
Query: 276 LILQ---EPIAKM----------EVLYGKYDEERTEKL---------------------- 300
L+ E IA M E + ++ E+L
Sbjct: 139 LVQGGKVEIIAMMKPERRLEIEEEAAGSREKRKKKERLKKLIEETENLAELIIDLEELKL 198
Query: 301 TRVQLVETDLKALEPELRKAVNFLELENCVQRKHNEIYQYERYVNMKNLGEHETKVQQME 360
++L E KALE K LE EN + + ++ + + + L + + +++ +
Sbjct: 199 QELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSK 258
Query: 361 QELTANLESIKKCTDEMESAKTELKTVE 388
QEL E + + E + + E K E
Sbjct: 259 QELEKEEEILAQVLKENKEEEKEKKLQE 286
Score = 37.3 bits (86), Expect = 0.013
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 100 GEVEQISMMPPKGKTEKETGLLEYLEEIIGTNRYKRF 136
G+VE I+MM P+ + E E E+ R K+
Sbjct: 143 GKVEIIAMMKPERRLEIEEEAAGSREKRKKKERLKKL 179
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 113 bits (284), Expect = 4e-27
Identities = 67/259 (25%), Positives = 122/259 (47%), Gaps = 36/259 (13%)
Query: 157 RFNAIIGPNGSGKSNVIDSMLFVFGYRASKI-RANKLSVLMHK-SDQVGGVSRCSVAIHF 214
F AI+GPNGSGKSN++D++ FV G +++K RA+K+S L+ S + V + F
Sbjct: 25 GFTAIVGPNGSGKSNIVDAIRFVLGEQSAKNLRASKMSDLIFAGSGNRKPANYAEVELTF 84
Query: 215 AQIIDKPNEEYEIIPGTDLEIARTAFYDNSSYYTLNGKKVHFKEVAKVLRDHGVDLLNNR 274
++ + ++ + R + D S Y +NG+KV K++ +L D G+ +
Sbjct: 85 -----DNSDNTLPLEYEEISVTRRIYRDGESEYYINGEKVRLKDIQDLLADSGIG-KESY 138
Query: 275 FLILQEPIAK------------MEVLYG--KYDEERTE----------KLTRVQL----V 306
++ Q + + +E G KY E + E L R++ +
Sbjct: 139 SIVSQGKVEEIINAKPEERRKLIEEAAGVSKYKERKEEAERKLERTEENLERLEDLLEEL 198
Query: 307 ETDLKALEPELRKAVNFLELENCVQRKHNEIYQYERYVNMKNLGEHETKVQQMEQELTAN 366
E L+ LE + KA + EL+ ++ + + K L E E ++ ++E+EL
Sbjct: 199 EKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKELEELEEELSRLEEELEEL 258
Query: 367 LESIKKCTDEMESAKTELK 385
E +++ E+E K+EL+
Sbjct: 259 QEELEEAEKEIEELKSELE 277
Score = 28.5 bits (64), Expect = 8.0
Identities = 32/136 (23%), Positives = 67/136 (49%), Gaps = 10/136 (7%)
Query: 256 FKEVAKVLRDHGVDLLNNRFLILQEPIAKMEVLYGKYDEERTEKLTRVQLVETDLKALE- 314
++E+ LR+ + LL + L++ + ++E + +EE E ++ E +++ L+
Sbjct: 215 YQELKAELRELELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKS 274
Query: 315 --PELRKAVNFLELENCVQRKHNEIYQYERYVNMKNLGEHETKVQQMEQELTANLESIKK 372
ELR+ + EL+ + EI + E + L E +++ +EL LE +K
Sbjct: 275 ELEELREELE--ELQEELLELKEEIEELEG--EISLLRERLEELENELEELEERLEELK- 329
Query: 373 CTDEMESAKTELKTVE 388
+++E+ K EL+ E
Sbjct: 330 --EKIEALKEELEERE 343
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 92.8 bits (231), Expect = 3e-20
Identities = 78/301 (25%), Positives = 127/301 (42%), Gaps = 58/301 (19%)
Query: 123 YLEEIIGTNRYKRFNAIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGKSNVIDSMLFVFGY 182
Y+E I N +K F GK VI F I GPNGSGKSN+ D++LF G
Sbjct: 1 YIERIELEN-FKSF---------GKKKVI-PFSKGFTVISGPNGSGKSNIGDAILFALGL 49
Query: 183 RASK-IRANKLSVLMHKSDQVGGVSRCSVAIHFAQIIDKPNEEYEIIPGTDLEIARTAFY 241
+SK +RA +LS L+ + V + F K +E E++ L++ Y
Sbjct: 50 SSSKAMRAERLSDLISNGKNGQSGNEAYVTVTFKNDDGKFPDELEVV--RRLKVTDDGKY 107
Query: 242 DNSSYYTLNGKKVHFKEVAKVLRDHGV--DLLNNRFLILQEPIAKM------------EV 287
SYY LNG++V E+ L G+ + N ++LQ + +
Sbjct: 108 ---SYYYLNGQRVRLSEIHDFLAAAGIYPEGYN---VVLQGDVTDFISMSPVERRKIIDE 161
Query: 288 LYG--KYDEERT---EKLTRVQLVETDLKALEPELRKAVNFLELENCVQRKHNEIYQ--- 339
+ G ++D ++ E+L V+ L + E R+ + L E R+ E YQ
Sbjct: 162 IAGVAEFDRKKEKALEELEEVEENIERLDLIIDEKRQQLERLRRE----REKAERYQALL 217
Query: 340 -----YERYVNMKNLGEHETKVQQMEQELTANLESIKKCT-------DEMESAKTELKTV 387
YE Y +K E + + +E++L + E ++K T +E + L+ +
Sbjct: 218 KEKREYEGYELLKEKEALERQKEAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEEL 277
Query: 388 E 388
Sbjct: 278 N 278
Score = 35.8 bits (83), Expect = 0.046
Identities = 18/95 (18%), Positives = 37/95 (38%), Gaps = 4/95 (4%)
Query: 294 EERTEKLTRVQLVETDLKALEPELRKAVNFLELENCVQRKHNEIYQYERYVNMKNLGEHE 353
EE + ++ V+ + EL+ LE ++R+ NE+ + E + L
Sbjct: 364 EELEDLRAELEEVDKEFAETRDELKDYREKLEK---LKREINEL-KRELDRLQEELQRLS 419
Query: 354 TKVQQMEQELTANLESIKKCTDEMESAKTELKTVE 388
++ + + I + +E E E+K E
Sbjct: 420 EELADLNAAIAGIEAKINELEEEKEDKALEIKKQE 454
>gnl|CDD|213242 cd03275, ABC_SMC1_euk, ATP-binding cassette domain of eukaryotic
SMC1 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 247
Score = 80.3 bits (199), Expect = 2e-17
Identities = 45/143 (31%), Positives = 64/143 (44%), Gaps = 16/143 (11%)
Query: 145 SGKSNVIDSMLFRFNAIIGPNGSGKSNVIDSMLFVFGYRASKIRANKLSVLMHKSDQVGG 204
S K + RF IIGPNGSGKSN++D++ FV G ++S +R+ L L++++
Sbjct: 11 SYKGRHVIGPFDRFTCIIGPNGSGKSNLMDAISFVLGEKSSHLRSKNLKDLIYRARVGKP 70
Query: 205 VSR-CSVAIHFAQIIDKPNEEYEIIPGTDLEIARTAFYDNSSYYTLNGKKVHFKEVAKVL 263
S V YE G + R SS Y +NGK V KE + L
Sbjct: 71 DSNSAYVTA-----------VYEDDDGEEKTFRRI-ITGGSSSYRINGKVVSLKEYNEEL 118
Query: 264 RDHGVDLLNNRFLILQ---EPIA 283
+ + FL+ Q E IA
Sbjct: 119 EKINILVKARNFLVFQGDVESIA 141
>gnl|CDD|213240 cd03273, ABC_SMC2_euk, ATP-binding cassette domain of eukaryotic
SMC2 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 251
Score = 78.5 bits (194), Expect = 1e-16
Identities = 49/147 (33%), Positives = 75/147 (51%), Gaps = 13/147 (8%)
Query: 158 FNAIIGPNGSGKSNVIDSMLFVFGYRA-SKIRANKLSVLMHKSDQVGGVSRCSVAIHFAQ 216
FNAI G NGSGKSN++D++ FV G S +RA+ L L++K Q G+++ SV I F
Sbjct: 27 FNAITGLNGSGKSNILDAICFVLGITNLSTVRASNLQDLIYKRGQ-AGITKASVTIVFDN 85
Query: 217 IIDKPN-----EEYEIIPGTDLEIARTAFYDNSSYYTLNGKKVHFKEVAKVLRDHGVDLL 271
DK E Y I + R ++ Y +NG + + V + + +++
Sbjct: 86 -SDKSQSPIGFENYPEI-----TVTRQIVLGGTNKYLINGHRAQQQRVQDLFQSVQLNVN 139
Query: 272 NNRFLILQEPIAKMEVLYGKYDEERTE 298
N FLI+Q I K+ + G + E TE
Sbjct: 140 NPHFLIMQGRITKVLNMGGVWKESLTE 166
>gnl|CDD|213206 cd03239, ABC_SMC_head, The SMC head domain belongs to the
ATP-binding cassette superfamily. The structural
maintenance of chromosomes (SMC) proteins are essential
for successful chromosome transmission during
replication and segregation of the genome in all
organisms. SMCs are generally present as single proteins
in bacteria, and as at least six distinct proteins in
eukaryotes. The proteins range in size from
approximately 110 to 170 kDa, and each has five distinct
domains: amino- and carboxy-terminal globular domains,
which contain sequences characteristic of ATPases, two
coiled-coil regions separating the terminal domains ,
and a central flexible hinge. SMC proteins function
together with other proteins in a range of chromosomal
transactions, including chromosome condensation,
sister-chromatid cohesion, recombination, DNA repair,
and epigenetic silencing of gene expression.
Length = 178
Score = 71.2 bits (175), Expect = 1e-14
Identities = 27/58 (46%), Positives = 38/58 (65%), Gaps = 1/58 (1%)
Query: 157 RFNAIIGPNGSGKSNVIDSMLFVFGYRASKIRANKLSVLMHKSDQVGGVSRCSVAIHF 214
FNAI+GPNGSGKSN++D++ FV G +A+K+R L L + G++ SV I F
Sbjct: 23 SFNAIVGPNGSGKSNIVDAICFVLGGKAAKLRRGSLLFLAGGGVK-AGINSASVEITF 79
>gnl|CDD|213245 cd03278, ABC_SMC_barmotin, ATP-binding cassette domain of barmotin,
a member of the SMC protein family. Barmotin is a tight
junction-associated protein expressed in rat epithelial
cells which is thought to have an important regulatory
role in tight junction barrier function. Barmotin
belongs to the SMC protein family. SMC proteins are
large (approximately 110 to 170 kDa), and each is
arranged into five recognizable domains. Amino-acid
sequence homology of SMC proteins between species is
largely confined to the amino- and carboxy-terminal
globular domains. The amino-terminal domain contains a
'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the
single-letter amino-acid code), which by mutational
studies has been shown to be essential in several
proteins. The carboxy-terminal domain contains a
sequence (the DA-box) that resembles a 'Walker B' motif,
and a motif with homology to the signature sequence of
the ATP-binding cassette (ABC) family of ATPases. The
sequence homology within the carboxy-terminal domain is
relatively high within the SMC1-SMC4 group, whereas SMC5
and SMC6 show some divergence in both of these
sequences. In eukaryotic cells, the proteins are found
as heterodimers of SMC1 paired with SMC3, SMC2 with
SMC4, and SMC5 with SMC6 (formerly known as Rad18).
Length = 197
Score = 66.7 bits (164), Expect = 5e-13
Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 158 FNAIIGPNGSGKSNVIDSMLFVFGYRASK-IRANKLS-VLMHKSDQVGGVSRCSVAIHFA 215
AI+GPNGSGKSN+ID++ +V G +++K +R K+S V+ S+ + V + F
Sbjct: 24 LTAIVGPNGSGKSNIIDAIRWVLGEQSAKSLRGEKMSDVIFAGSETRKPANFAEVTLTF- 82
Query: 216 QIIDKPNEEYEII 228
D + Y II
Sbjct: 83 ---DNSDGRYSII 92
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 66.6 bits (163), Expect = 8e-12
Identities = 67/273 (24%), Positives = 120/273 (43%), Gaps = 57/273 (20%)
Query: 152 DSMLFRFN----AIIGPNGSGKSNVIDSMLFVFGYRASK-IRANKLS-VLMHKSDQVGGV 205
D F+ I+GPNG GKSN++D++ +V G +++K +R K+ V+ + S+ +
Sbjct: 15 DPTTINFDKGITGIVGPNGCGKSNIVDAIRWVLGEQSAKALRGGKMEDVIFNGSETRKPL 74
Query: 206 SRCSVAIHFAQIIDKPNEEYEIIPGTD---LEIARTAFYDNSSYYTLNGKKVHFKEVAKV 262
S V + F + ++PG D + I R + D S Y +NG+ K++ +
Sbjct: 75 SLAEVELVF-------DNSDGLLPGADYSEISITRRLYRDGESEYFINGQPCRLKDIQDL 127
Query: 263 LRDHGV--------------DLLN----NRFLILQEPIAKMEVLYGKYDEERTEKLTRVQ 304
D G+ +++ R I +E KY E R E +++
Sbjct: 128 FLDTGLGKRSYSIIEQGKISEIIEAKPEERRAIFEEAAG-----ISKYKERRKETERKLE 182
Query: 305 LVETDLKALEP---ELRKAVNFLELENCVQRKHNEIYQYERYVNMKN-LGEHE-----TK 355
+L LE EL + + LE Q + + ERY +K L E E +
Sbjct: 183 RTRENLDRLEDILNELERQLKSLER----QAE-----KAERYKELKAELRELELALLVLR 233
Query: 356 VQQMEQELTANLESIKKCTDEMESAKTELKTVE 388
++++ +EL E +K+ +E+E EL+ +E
Sbjct: 234 LEELREELEELQEELKEAEEELEELTAELQELE 266
Score = 32.7 bits (75), Expect = 0.43
Identities = 31/140 (22%), Positives = 63/140 (45%), Gaps = 10/140 (7%)
Query: 256 FKEVAKVLRDHGVDLLNNRFLILQEPIAKMEVLYGKYDEERTEKLTRVQLVETDLKALE- 314
+KE+ LR+ + LL R L+E + +++ + +EE E +Q +E L+ L
Sbjct: 215 YKELKAELRELELALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEELRL 274
Query: 315 --PELRKAVN-----FLELENCVQRKHNEI--YQYERYVNMKNLGEHETKVQQMEQELTA 365
EL + + L N + R + + + L E E +++++E +L
Sbjct: 275 EVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDE 334
Query: 366 NLESIKKCTDEMESAKTELK 385
E + + +++E K EL+
Sbjct: 335 LAEELAELEEKLEELKEELE 354
Score = 29.6 bits (67), Expect = 3.7
Identities = 17/91 (18%), Positives = 37/91 (40%), Gaps = 7/91 (7%)
Query: 294 EERTEKLTRVQLVETDLKALEPELRKAVNFLELENCVQRKHNEIYQYERYVNMKNLGEHE 353
EE +E + + +L+ L EL + L E + + + E + L E E
Sbjct: 848 EELSEDIESLAAEIEELEELIEELESELEALLNERASLEEALALLRSELEELSEELRELE 907
Query: 354 TKVQQMEQELTANLESIKKCTDEMESAKTEL 384
+K ++ +EL ++ +++ + L
Sbjct: 908 SKRSELRREL-------EELREKLAQLELRL 931
Score = 28.5 bits (64), Expect = 7.5
Identities = 26/111 (23%), Positives = 45/111 (40%), Gaps = 11/111 (9%)
Query: 278 LQEPIAKMEVLYGKYDEERTEKLTRVQLVETDLKALEPELRKAVNFLELENCVQRKHNEI 337
L+E I ++E E+ E + + +L+ LE EL + ELE ++
Sbjct: 682 LEEKIEELE-------EKIAELEKALAELRKELEELEEELEQLR--KELEELSRQISALR 732
Query: 338 YQYERYVNMKNLGEHETKVQQMEQELTANLESIKKCTDEMESAKTELKTVE 388
R E + Q+ +ELT I++ + +E A+ EL E
Sbjct: 733 KDLARLEAEVEQLEER--IAQLSKELTELEAEIEELEERLEEAEEELAEAE 781
>gnl|CDD|213194 cd03227, ABC_Class2, ATP-binding cassette domain of non-transporter
proteins. ABC-type Class 2 contains systems involved in
cellular processes other than transport. These families
are characterized by the fact that the ABC subunit is
made up of duplicated, fused ABC modules (ABC2). No
known transmembrane proteins or domains are associated
with these proteins.
Length = 162
Score = 52.4 bits (126), Expect = 3e-08
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 8/64 (12%)
Query: 157 RFNAIIGPNGSGKSNVIDSMLFVFGYRASKIRANKLSVLMHKSDQVGGVSRCSVAIHFAQ 216
I GPNGSGKS ++D++ G S R + G + +V+
Sbjct: 22 SLTIITGPNGSGKSTILDAIGLALGGAQSATRR-------RSGVKAGCIV-AAVSAELIF 73
Query: 217 IIDK 220
+
Sbjct: 74 TRLQ 77
Score = 41.2 bits (97), Expect = 2e-04
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 135 RFNAIIGPNGSGKSNVIDSMLF 156
I GPNGSGKS ++D++
Sbjct: 22 SLTIITGPNGSGKSTILDAIGL 43
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 46.8 bits (111), Expect = 4e-06
Identities = 32/206 (15%), Positives = 77/206 (37%), Gaps = 23/206 (11%)
Query: 158 FNAIIGPNGSGKSNVIDSMLFVFGYRASKIRANKLSVLMHKSDQVGGVSRCSVAIHFAQI 217
I GPNGSGK+ ++D++ + + S+++ +K ++ I +
Sbjct: 21 LTLIYGPNGSGKTTILDAIRWALYGKTSRLKKSKGRGIVKGD------------IEIEKD 68
Query: 218 IDKPNEEYEIIPGTDLEIARTAFYDNSSYYTLNGKKVHFKEVAKVLRDHGVDLLNNRFLI 277
K EI + + + S T K K + +++ + + L
Sbjct: 69 EGKKKTYVEITFENNKGKLKLRLIEESRELTKKKGKKVKKSILEIVEIDELQEFIDELLK 128
Query: 278 LQEPIAKMEVLYGKYDEERTEKLTRVQLVETDLKALEPELRKAVNFLELENCVQRKHNEI 337
+ I + + G+ E + + + L+ LE EL + + +L + + +
Sbjct: 129 SDKEILPLLLYLGQERLEELKFKRKEKK--ERLEELEKELEELEDEKDLLEKLLEEKEKK 186
Query: 338 YQYERYVNMKNLGEHETKVQQMEQEL 363
+ E + +++++ +EL
Sbjct: 187 KELEEL---------KEELEELLEEL 203
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 46.3 bits (109), Expect = 1e-05
Identities = 30/147 (20%), Positives = 51/147 (34%), Gaps = 5/147 (3%)
Query: 136 FNAIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGKSNVIDSMLFVFGYRASKIRANKLSVL 195
N IIGPNGSGKSN++ ++ + + + L F ++I L
Sbjct: 1 LNVIIGPNGSGKSNLLKALALLLLLLSLGLTLDRGLNVGIKLLPFLLDENEIE-IPLEFE 59
Query: 196 MHKSDQVGGVSRCSVAIHFAQIIDKPNEEYEIIPGTDLEIARTAFYDNSSYYTLNGKKVH 255
+ + G R + I+ EE E+ S+ KK
Sbjct: 60 IEEFLIDGIRYRYGFELDKEDIL----EELLYEYRKGEELLFERERSKESFEKSPEKKRE 115
Query: 256 FKEVAKVLRDHGVDLLNNRFLILQEPI 282
+ + +VL + L + L E +
Sbjct: 116 LRGLREVLLLLNLSLSSFLLLASLEIL 142
>gnl|CDD|213208 cd03241, ABC_RecN, ATP-binding cassette domain of RecN. RecN
ATPase involved in DNA repair; similar to ABC
(ATP-binding cassette) transporter nucleotide-binding
domain; ABC transporters are a large family of proteins
involved in the transport of a wide variety of different
compounds including sugars, ions, peptides, and more
complex organic molecules. The nucleotide binding domain
shows the highest similarity between all members of the
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 276
Score = 44.5 bits (106), Expect = 4e-05
Identities = 32/121 (26%), Positives = 46/121 (38%), Gaps = 25/121 (20%)
Query: 158 FNAIIGPNGSGKSNVIDSMLFVFGYRASK--IRANKLSVLMHKSDQVGGVSRCSVAIHFA 215
+ G G+GKS ++D++ + G RAS IR+ G + V F
Sbjct: 23 LTVLTGETGAGKSILLDALSLLLGGRASADLIRS--------------GAEKAVVEGVF- 67
Query: 216 QIIDKPNE------EYEIIPGTDLEIARTAFYDNSSYYTLNGKKVHFKEVAKVLRDHGVD 269
I E E I DL I R S Y +NG+ V K + + L VD
Sbjct: 68 -DISDEEEAKALLLELGIEDDDDLIIRREISRKGRSRYFINGQSVTLKLLRE-LGSLLVD 125
Query: 270 L 270
+
Sbjct: 126 I 126
>gnl|CDD|205733 pfam13555, AAA_29, P-loop containing region of AAA domain.
Length = 60
Score = 39.9 bits (94), Expect = 9e-05
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 157 RFNAIIGPNGSGKSNVIDSMLFVFGYRASKIRANK 191
+ + GP+GSGKS +ID++ + A ++ NK
Sbjct: 22 KGTLLTGPSGSGKSTLIDAIQTLL-VPAKRVAFNK 55
Score = 34.5 bits (80), Expect = 0.006
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 8/34 (23%)
Query: 135 RFNAIIGPNGSGKSNVIDSMLF--------RFNA 160
+ + GP+GSGKS +ID++ FN
Sbjct: 22 KGTLLTGPSGSGKSTLIDAIQTLLVPAKRVAFNK 55
>gnl|CDD|213239 cd03272, ABC_SMC3_euk, ATP-binding cassette domain of eukaryotic
SMC3 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 243
Score = 39.6 bits (93), Expect = 0.001
Identities = 35/138 (25%), Positives = 60/138 (43%), Gaps = 11/138 (7%)
Query: 150 VIDSMLFRFNAIIGPNGSGKSNVIDSMLFVFGYRASKIRANKLSVLMHKSDQVGGVSRCS 209
VI+ + N ++G NGSGKSN ++ FV + +R + L+H+ S S
Sbjct: 17 VIEPFSPKHNVVVGRNGSGKSNFFAAIRFVLSDEYTHLREEQRQALLHEG------SGPS 70
Query: 210 VAIHFAQIIDKPNEEYEIIPGTDLEIART--AFYDNSSYYTLNGKKVHFKEVAKVLRDHG 267
V + +II ++ I ++ + RT D Y L+ K V +V +L G
Sbjct: 71 VMSAYVEIIFDNSDNRFPIDKEEVRLRRTIGLKKD---EYFLDKKNVTKNDVMNLLESAG 127
Query: 268 VDLLNNRFLILQEPIAKM 285
N +++ Q I +
Sbjct: 128 FSRSNPYYIVPQGKINSL 145
Score = 31.5 bits (72), Expect = 0.58
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 123 YLEEIIGTNRYKRFNAIIGPNGSGKSNVIDSMLF 156
Y ++ + + N ++G NGSGKSN ++ F
Sbjct: 12 YKDQTVIEPFSPKHNVVVGRNGSGKSNFFAAIRF 45
>gnl|CDD|213244 cd03277, ABC_SMC5_euk, ATP-binding cassette domain of eukaryotic
SMC5 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 213
Score = 38.0 bits (89), Expect = 0.004
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 152 DSMLFRF----NAIIGPNGSGKSNVIDSMLFVFGYRASKI-RANKL 192
D FR N IIGPNGSGKS+++ ++ G + + RA K+
Sbjct: 15 DETEFRPGPSLNMIIGPNGSGKSSIVCAICLGLGGKPKLLGRAKKV 60
Score = 33.3 bits (77), Expect = 0.13
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 134 KRFNAIIGPNGSGKSNVI 151
N IIGPNGSGKS+++
Sbjct: 23 PSLNMIIGPNGSGKSSIV 40
>gnl|CDD|213243 cd03276, ABC_SMC6_euk, ATP-binding cassette domain of eukaryotic
SM6 proteins. The structural maintenance of chromosomes
(SMC) proteins are large (approximately 110 to 170 kDa),
and each is arranged into five recognizable domains.
Amino-acid sequence homology of SMC proteins between
species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 198
Score = 36.8 bits (86), Expect = 0.009
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 152 DSMLFRF----NAIIGPNGSGKSNVIDSMLFVFGYRASKI-RANKLS 193
+ F N I+G NGSGKS ++ ++ G +AS R + L
Sbjct: 13 RHLQIEFGPRVNFIVGNNGSGKSAILTALTIGLGGKASDTNRGSSLK 59
Score = 29.9 bits (68), Expect = 1.5
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 134 KRFNAIIGPNGSGKSNVI 151
R N I+G NGSGKS ++
Sbjct: 21 PRVNFIVGNNGSGKSAIL 38
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 37.8 bits (88), Expect = 0.009
Identities = 53/272 (19%), Positives = 99/272 (36%), Gaps = 52/272 (19%)
Query: 158 FNAIIGPNGSGKSNVIDSMLFVFGYRASKIRANKLSVLMHKSDQVGGVSRCSVAIHF--- 214
I+GPNG+GKS+++D++ F + ++ A L L+ G SV + F
Sbjct: 27 IFLIVGPNGAGKSSILDAITFALYGKTPRLGAFSLDDLIRA-----GEKSASVELEFEVN 81
Query: 215 ----------------------------AQIIDKPNEEYEIIP---GTDLEIARTAFY-- 241
+I D + E I G D + + Y
Sbjct: 82 GKKYRIEREFRRGRGQSTGSLQIIEVDGERIADGKKDVNEKIEELLGLDKDTFTRSVYLP 141
Query: 242 DNSSYYTLNGKKVHFKE-VAKVLR-DHGVDLLNNRFLILQEPIAKMEVLYGKYDE--ERT 297
L K KE + ++ + L +++E AK+E L G+ E E
Sbjct: 142 QGEFDAFLKSKPKERKEILDELFGLEKYEKLSELLKEVIKEAKAKIEELEGQLSELLEDI 201
Query: 298 EKLTRVQLVETDLKALEPELRKAVNFLELENCVQRKHNEIYQYERYVNMKNLGEHETKVQ 357
E L E E+++ ELE + + ER ++ E +++
Sbjct: 202 EDLLEALEEELKELKKLEEIQEEQEEEELEQ----EIEAL--EERLAELEEEKERLEELK 255
Query: 358 -QMEQELTANLESIKKCTDEMESAKTELKTVE 388
++ + + LE++K +E+ + L+ +E
Sbjct: 256 ARLLEIESLELEALKIREEELRELERLLEELE 287
Score = 30.5 bits (69), Expect = 1.9
Identities = 23/106 (21%), Positives = 48/106 (45%), Gaps = 11/106 (10%)
Query: 294 EERTEKLTRVQLVETDLKALEPELRKAVNFLELENCVQRKHNEIYQYERYVNMKN----- 348
+E +KL ++ + L+ L L + ELE + +E+ + ++
Sbjct: 596 KELKKKLKELEERLSQLEELLQSLELSEAENELEEAEEELESELEKLNLQAELEELLQAA 655
Query: 349 LGEHETKVQQMEQEL------TANLESIKKCTDEMESAKTELKTVE 388
L E E KV+++E E+ N E +++ +E+E + EL+ +
Sbjct: 656 LEELEEKVEELEAEIRRELQRIENEEQLEEKLEELEQLEEELEQLR 701
Score = 30.1 bits (68), Expect = 2.5
Identities = 21/113 (18%), Positives = 45/113 (39%), Gaps = 3/113 (2%)
Query: 272 NNRFLILQEPIAKMEVLYGKYDEERTEKLTRVQLVETDLKALEPELRKAVNFLELENCVQ 331
+ ++E + EE+ EKL L+E +L+ L+ +L+ EL
Sbjct: 510 LRELEEELIELLELEEALKEELEEKLEKLE--NLLE-ELEELKEKLQLQQLKEELRQLED 566
Query: 332 RKHNEIYQYERYVNMKNLGEHETKVQQMEQELTANLESIKKCTDEMESAKTEL 384
R E ++ E ++++ +EL L+ +++ ++E L
Sbjct: 567 RLQELKELLEELRLLRTRKEELEELRERLKELKKKLKELEERLSQLEELLQSL 619
>gnl|CDD|224031 COG1106, COG1106, Predicted ATPases [General function prediction
only].
Length = 371
Score = 36.7 bits (85), Expect = 0.016
Identities = 10/33 (30%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 147 KSNVIDSMLFRFNAIIGPNGSGKSNVIDSMLFV 179
+ ++ + N I G NG+GKSN+++++ F+
Sbjct: 14 RELELEDFG-KINIIYGANGAGKSNLLEALYFL 45
Score = 35.6 bits (82), Expect = 0.040
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 132 RYKRFNAIIGPNGSGKSNVIDSMLF 156
+ + N I G NG+GKSN+++++ F
Sbjct: 20 DFGKINIIYGANGAGKSNLLEALYF 44
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 35.3 bits (82), Expect = 0.017
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 157 RFNAIIGPNGSGKSNVIDSMLFVFGYRASKIR 188
A++GPNGSGKS ++ ++ + + +I
Sbjct: 26 EIVALVGPNGSGKSTLLRAIAGLLKPTSGEIL 57
Score = 33.8 bits (78), Expect = 0.057
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 135 RFNAIIGPNGSGKSNVIDSMLF 156
A++GPNGSGKS ++ ++
Sbjct: 26 EIVALVGPNGSGKSTLLRAIAG 47
>gnl|CDD|213202 cd03235, ABC_Metallic_Cations, ATP-binding cassette domain of the
metal-type transporters. This family includes
transporters involved in the uptake of various metallic
cations such as iron, manganese, and zinc. The ATPases
of this group of transporters are very similar to
members of iron-siderophore uptake family suggesting
that they share a common ancestor. The best
characterized metal-type ABC transporters are the
YfeABCD system of Y. pestis, the SitABCD system of
Salmonella enterica serovar Typhimurium, and the SitABCD
transporter of Shigella flexneri. Moreover other
uncharacterized homologs of these metal-type
transporters are mainly found in pathogens like
Haemophilus or enteroinvasive E. coli isolates.
Length = 213
Score = 36.0 bits (84), Expect = 0.020
Identities = 21/55 (38%), Positives = 26/55 (47%), Gaps = 16/55 (29%)
Query: 136 FNAIIGPNGSGKSNVIDSMLFRFNAIIG--PNGSGKSNVIDSMLFVFGYRASKIR 188
F AI+GPNG+GKS L + AI+G SG + VFG K R
Sbjct: 27 FLAIVGPNGAGKST-----LLK--AILGLLKPTSGS-------IRVFGKPLEKER 67
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 35.7 bits (83), Expect = 0.046
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 158 FNAIIGPNGSGKSNVIDSMLFVFGYRAS 185
+ G G+GKS +ID++ + G RA
Sbjct: 24 LTVLTGETGAGKSIIIDALGLLLGGRAD 51
>gnl|CDD|226929 COG4559, COG4559, ABC-type hemin transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 259
Score = 34.6 bits (80), Expect = 0.054
Identities = 32/156 (20%), Positives = 63/156 (40%), Gaps = 34/156 (21%)
Query: 159 NAIIGPNGSGKSNVIDSMLFVFGYRASKIRANKLSVLMHKSDQVG---GVSRCSVAIHFA 215
AI+GPNG+GKS ++ ++ + ++ N + + +++ V + ++ F
Sbjct: 30 LAILGPNGAGKSTLLKALSGELSPDSGEVTLNGVPLNSWPPEELARHRAVLPQNSSLAF- 88
Query: 216 QIIDKPNEEYEII------------PGTDLEIARTAF-------YDNSSYYTLNG---KK 253
P E++ P D IA A Y TL+G ++
Sbjct: 89 -----PFTVQEVVQMGRIPHRSGREPEEDERIAAQALAATDLSGLAGRDYRTLSGGEQQR 143
Query: 254 VHFKEVAKVLRDHGVDLLNNRFLILQEPIAKMEVLY 289
V A+VL + + R+L L EP + +++ +
Sbjct: 144 VQL---ARVLAQLWPPVPSGRWLFLDEPTSALDIAH 176
>gnl|CDD|213207 cd03240, ABC_Rad50, ATP-binding cassette domain of Rad50. The
catalytic domains of Rad50 are similar to the
ATP-binding cassette of ABC transporters, but are not
associated with membrane-spanning domains. The conserved
ATP-binding motifs common to Rad50 and the ABC
transporter family include the Walker A and Walker B
motifs, the Q loop, a histidine residue in the switch
region, a D-loop, and a conserved LSGG sequence. This
conserved sequence, LSGG, is the most specific and
characteristic motif of this family and is thus known as
the ABC signature sequence.
Length = 204
Score = 34.5 bits (80), Expect = 0.056
Identities = 19/86 (22%), Positives = 32/86 (37%), Gaps = 12/86 (13%)
Query: 158 FNAIIGPNGSGKSNVIDSMLFV-FGYRASKIRANKLSVLMHKSDQVG-GVSRCSVAIHFA 215
I+G NG+GK+ +I+++ + G +K H + G R V + F
Sbjct: 24 LTLIVGQNGAGKTTIIEALKYALTG---ELPPNSKGGA--HDPKLIREGEVRAQVKLAFE 78
Query: 216 QIIDKPNEEYEIIPGTDLEIARTAFY 241
K +Y I L I +
Sbjct: 79 NANGK---KYTIT--RSLAILENVIF 99
Score = 34.1 bits (79), Expect = 0.063
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 136 FNAIIGPNGSGKSNVIDSMLF 156
I+G NG+GK+ +I+++ +
Sbjct: 24 LTLIVGQNGAGKTTIIEALKY 44
>gnl|CDD|234608 PRK00064, recF, recombination protein F; Reviewed.
Length = 361
Score = 35.1 bits (82), Expect = 0.057
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 135 RFNAIIGPNGSGKSNVI 151
N ++G NG GK+N++
Sbjct: 24 GVNVLVGENGQGKTNLL 40
Score = 35.1 bits (82), Expect = 0.057
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 157 RFNAIIGPNGSGKSNVI 173
N ++G NG GK+N++
Sbjct: 24 GVNVLVGENGQGKTNLL 40
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 34.4 bits (80), Expect = 0.059
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 9/46 (19%)
Query: 136 FNAIIGPNGSGKSNVIDSMLFRFNAIIG--PNGSGKSNVIDSMLFV 179
AI+GP GSGKS S+L +A++G SG +V S+ +V
Sbjct: 33 LVAIVGPVGSGKS----SLL---SALLGELEKLSGSVSVPGSIAYV 71
>gnl|CDD|226984 COG4637, COG4637, Predicted ATPase [General function prediction
only].
Length = 373
Score = 34.8 bits (80), Expect = 0.063
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 151 IDSMLFRFNAIIGPNGSGKSNVIDSMLFV 179
+D + R N IIG NG+GKSN D++ +
Sbjct: 17 LDLEIRRVNVIIGANGAGKSNFYDALRLL 45
Score = 33.2 bits (76), Expect = 0.21
Identities = 13/24 (54%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 135 RFNAIIGPNGSGKSNVIDSMLFRF 158
R N IIG NG+GKSN D R
Sbjct: 23 RVNVIIGANGAGKSNFYD--ALRL 44
>gnl|CDD|224046 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component
[Inorganic ion transport and metabolism].
Length = 254
Score = 34.1 bits (79), Expect = 0.079
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 10/45 (22%)
Query: 158 FNAIIGPNGSGKSNVIDSML----------FVFGYRASKIRANKL 192
A+IGPNG+GKS ++ ++L +FG K R
Sbjct: 32 ITALIGPNGAGKSTLLKAILGLLKPSSGEIKIFGKPVRKRRKRLR 76
Score = 33.0 bits (76), Expect = 0.20
Identities = 10/20 (50%), Positives = 16/20 (80%)
Query: 136 FNAIIGPNGSGKSNVIDSML 155
A+IGPNG+GKS ++ ++L
Sbjct: 32 ITALIGPNGAGKSTLLKAIL 51
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
metabolism, Restriction/modification].
Length = 650
Score = 34.7 bits (80), Expect = 0.093
Identities = 26/127 (20%), Positives = 53/127 (41%), Gaps = 8/127 (6%)
Query: 265 DHGVDLLNNRFLILQEPIAKMEVLYGKYDEERTEKLTRVQLVETDL----KALEPELRKA 320
+H ++ I + E+ + E T+ +Q V+ +L L ELR+
Sbjct: 344 EHVKEIAAELAEIDKPATTDSEIPHRLSGSELTQLEVLIQQVKRELQDAKSQLLKELRE- 402
Query: 321 VNFLELENCVQRKHNEIYQYERYVNM-KNLGEHETKVQQMEQELTANLESIKKCTDEMES 379
EL V +K + I E+ + + LGE + ++ + E E+ L ++ + +E+
Sbjct: 403 -LEEELAE-VDKKISTIPSEEQIAQLLEELGEAQNELFRSEAEIEELLRQLETLKEAIEA 460
Query: 380 AKTELKT 386
+ L
Sbjct: 461 LRKTLDE 467
>gnl|CDD|233051 TIGR00611, recf, recF protein. All proteins in this family for
which functions are known are DNA binding proteins that
assist the filamentation of RecA onto DNA for the
initiation of recombination or recombinational repair.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 365
Score = 34.3 bits (79), Expect = 0.096
Identities = 9/22 (40%), Positives = 17/22 (77%)
Query: 135 RFNAIIGPNGSGKSNVIDSMLF 156
N I+GPNG GK+N+++++ +
Sbjct: 24 GVNVIVGPNGQGKTNLLEAIYY 45
Score = 34.3 bits (79), Expect = 0.096
Identities = 9/22 (40%), Positives = 17/22 (77%)
Query: 157 RFNAIIGPNGSGKSNVIDSMLF 178
N I+GPNG GK+N+++++ +
Sbjct: 24 GVNVIVGPNGQGKTNLLEAIYY 45
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component of
iron-siderophores, vitamin B12 and hemin transporters
and related proteins. ABC transporters, involved in the
uptake of siderophores, heme, and vitamin B12, are
widely conserved in bacteria and archaea. Only very few
species lack representatives of the siderophore family
transporters. The E. coli BtuCD protein is an ABC
transporter mediating vitamin B12 uptake. The two
ATP-binding cassettes (BtuD) are in close contact with
each other, as are the two membrane-spanning subunits
(BtuC); this arrangement is distinct from that observed
for the E. coli lipid flippase MsbA. The BtuC subunits
provide 20 transmembrane helices grouped around a
translocation pathway that is closed to the cytoplasm by
a gate region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 33.2 bits (77), Expect = 0.11
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 135 RFNAIIGPNGSGKSNVIDSML 155
I+GPNG+GKS ++ ++
Sbjct: 26 EIVGILGPNGAGKSTLLKTLA 46
Score = 33.2 bits (77), Expect = 0.11
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 157 RFNAIIGPNGSGKSNVIDSML 177
I+GPNG+GKS ++ ++
Sbjct: 26 EIVGILGPNGAGKSTLLKTLA 46
>gnl|CDD|213186 cd03219, ABC_Mj1267_LivG_branched, ATP-binding cassette component
of branched chain amino acids transport system. The
Mj1267/LivG ABC transporter subfamily is involved in the
transport of the hydrophobic amino acids leucine,
isoleucine and valine. MJ1267 is a branched-chain amino
acid transporter with 29% similarity to both the LivF
and LivG components of the E. coli branched-chain amino
acid transporter. MJ1267 contains an insertion from
residues 114 to 123 characteristic of LivG
(Leucine-Isoleucine-Valine) homologs. The branched-chain
amino acid transporter from E. coli comprises a
heterodimer of ABCs (LivF and LivG), a heterodimer of
six-helix TM domains (LivM and LivH), and one of two
alternative soluble periplasmic substrate binding
proteins (LivK or LivJ).
Length = 236
Score = 33.6 bits (78), Expect = 0.11
Identities = 9/17 (52%), Positives = 13/17 (76%), Gaps = 3/17 (17%)
Query: 138 AIIGPNGSGKS---NVI 151
+IGPNG+GK+ N+I
Sbjct: 30 GLIGPNGAGKTTLFNLI 46
Score = 33.6 bits (78), Expect = 0.11
Identities = 9/17 (52%), Positives = 13/17 (76%), Gaps = 3/17 (17%)
Query: 160 AIIGPNGSGKS---NVI 173
+IGPNG+GK+ N+I
Sbjct: 30 GLIGPNGAGKTTLFNLI 46
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 33.7 bits (78), Expect = 0.13
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 136 FNAIIGPNGSGKS 148
I+GPNGSGKS
Sbjct: 30 ITGILGPNGSGKS 42
Score = 33.7 bits (78), Expect = 0.13
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 158 FNAIIGPNGSGKS 170
I+GPNGSGKS
Sbjct: 30 ITGILGPNGSGKS 42
>gnl|CDD|213246 cd03279, ABC_sbcCD, ATP-binding cassette domain of sbcCD. SbcCD
and other Mre11/Rad50 (MR) complexes are implicated in
the metabolism of DNA ends. They cleave ends sealed by
hairpin structures and are thought to play a role in
removing protein bound to DNA termini.
Length = 213
Score = 33.0 bits (76), Expect = 0.16
Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 12/78 (15%)
Query: 160 AIIGPNGSGKSNVIDSMLF-VFGYRASKIRANKLSVLMHKSDQVGGVSRCSVAIHFAQII 218
I GP G+GKS ++D++ + ++G R L + + V+ F
Sbjct: 32 LICGPTGAGKSTILDAITYALYGKTPRYGRQENLRSVFAPGED-----TAEVSFTFQL-- 84
Query: 219 DKPNEEYEII--PGTDLE 234
++Y + G D +
Sbjct: 85 --GGKKYRVERSRGLDYD 100
Score = 31.9 bits (73), Expect = 0.37
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 138 AIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGKSNVID 174
I GP G+GKS ++D++ + A+ G +
Sbjct: 32 LICGPTGAGKSTILDAITY---ALYG-KTPRYGRQEN 64
>gnl|CDD|237422 PRK13548, hmuV, hemin importer ATP-binding subunit; Provisional.
Length = 258
Score = 33.2 bits (77), Expect = 0.16
Identities = 9/11 (81%), Positives = 11/11 (100%)
Query: 138 AIIGPNGSGKS 148
AI+GPNG+GKS
Sbjct: 32 AILGPNGAGKS 42
Score = 33.2 bits (77), Expect = 0.16
Identities = 9/11 (81%), Positives = 11/11 (100%)
Query: 160 AIIGPNGSGKS 170
AI+GPNG+GKS
Sbjct: 32 AILGPNGAGKS 42
>gnl|CDD|188394 TIGR03864, PQQ_ABC_ATP, ABC transporter, ATP-binding subunit,
PQQ-dependent alcohol dehydrogenase system. Members of
this protein family are the ATP-binding subunit of an
ABC transporter system that is associated with PQQ
biosynthesis and PQQ-dependent alcohol dehydrogenases.
While this family shows homology to several efflux ABC
transporter subunits, the presence of a periplasmic
substrate-binding protein and association with systems
for catabolism of alcohols suggests a role in import
rather than detoxification [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 236
Score = 33.0 bits (76), Expect = 0.19
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 146 GKSNVIDSMLF-----RFNAIIGPNGSGKSNVIDSMLFVFGYRASKIR 188
G +D + F RF A++GPNG+GKS + + ++ + +I
Sbjct: 12 GARRALDDVSFTVRPGRFVALLGPNGAGKSTLFSLLTRLYVAQEGQIS 59
Score = 32.7 bits (75), Expect = 0.22
Identities = 13/23 (56%), Positives = 18/23 (78%), Gaps = 1/23 (4%)
Query: 135 RFNAIIGPNGSGKSNVIDSMLFR 157
RF A++GPNG+GKS + S+L R
Sbjct: 28 RFVALLGPNGAGKSTLF-SLLTR 49
>gnl|CDD|185067 PRK15112, PRK15112, antimicrobial peptide ABC system ATP-binding
protein SapF; Provisional.
Length = 267
Score = 32.8 bits (75), Expect = 0.23
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 14/79 (17%)
Query: 118 TGL-----LEYLEEIIGTNRYKRFNAIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGKSNV 172
TG +E ++ + T R + AIIG NGSGKS + ML +I P + +
Sbjct: 18 TGWFRRQTVEAVKPLSFTLREGQTLAIIGENGSGKST-LAKML---AGMIEP--TSGELL 71
Query: 173 IDSMLFVFG---YRASKIR 188
ID FG YR+ +IR
Sbjct: 72 IDDHPLHFGDYSYRSQRIR 90
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 33.4 bits (77), Expect = 0.23
Identities = 19/125 (15%), Positives = 41/125 (32%), Gaps = 15/125 (12%)
Query: 214 FAQIIDKPNEEYEIIPGTDLEIARTAFYDNSSYYTLNGKKVHFKEVAKVLRDHGVDLLNN 273
F + + E + + + Y + K EV + L+ G +
Sbjct: 148 FVGTVPEDKLEELKLESDVENVEYISTDKGYVYVVVVVLKELSDEVEEELKKLGFE---- 203
Query: 274 RFLILQEPIAKMEVLY-GKYDEERTEKLTRVQLVETDLKALEPELRKAVNFLELENCVQR 332
++E+ G E E ++ +E + ++L EL++ E
Sbjct: 204 ----------RLELEEEGTPSELIREIKEELEEIEKERESLLEELKELAKKYLEELLALY 253
Query: 333 KHNEI 337
++ EI
Sbjct: 254 EYLEI 258
>gnl|CDD|233209 TIGR00958, 3a01208, Conjugate Transporter-2 (CT2) Family protein.
[Transport and binding proteins, Other].
Length = 711
Score = 33.2 bits (76), Expect = 0.28
Identities = 10/21 (47%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 138 AIIGPNGSGKSNVIDSMLFRF 158
A++GP+GSGKS V ++L
Sbjct: 511 ALVGPSGSGKSTVA-ALLQNL 530
Score = 31.2 bits (71), Expect = 0.91
Identities = 10/18 (55%), Positives = 15/18 (83%), Gaps = 1/18 (5%)
Query: 160 AIIGPNGSGKSNVIDSML 177
A++GP+GSGKS V ++L
Sbjct: 511 ALVGPSGSGKSTVA-ALL 527
>gnl|CDD|224044 COG1119, ModF, ABC-type molybdenum transport system, ATPase
component/photorepair protein PhrA [Inorganic ion
transport and metabolism].
Length = 257
Score = 32.3 bits (74), Expect = 0.36
Identities = 28/170 (16%), Positives = 52/170 (30%), Gaps = 64/170 (37%)
Query: 160 AIIGPNGSGKSNVI----------DSMLFVFGYR------ASKIRANKLSVLMHKSDQVG 203
AI+GPNG+GK+ ++ + + G R ++R +G
Sbjct: 61 AIVGPNGAGKTTLLSLLTGEHPPSSGDVTLLGRRFGKGETIFELRKR-----------IG 109
Query: 204 GVSRCSVAIHFAQIIDKPNEEYEIIPGTDLEIARTAFYDNSSYYTLNGKKVHFKEVAKVL 263
VS + F + E T ++ + F+ + Y + +L
Sbjct: 110 LVSS-ELHERF-----RVRE-------TVRDVVLSGFFASIGIYQEDLTAEDLAAAQWLL 156
Query: 264 RDHGVDLLNNR------------------------FLILQEPIAKMEVLY 289
G L +R LIL EP ++++
Sbjct: 157 ELLGAKHLADRPFGSLSQGEQRRVLIARALVKDPELLILDEPAQGLDLIA 206
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They belong
to the subfamily C of the ATP-binding cassette (ABC)
superfamily of transport proteins. The ABCC subfamily
contains transporters with a diverse functional spectrum
that includes ion transport, cell surface receptor, and
toxin secretion activities. The MRP-like family, similar
to all ABC proteins, have a common four-domain core
structure constituted by two membrane-spanning domains,
each composed of six transmembrane (TM) helices, and two
nucleotide-binding domains (NBD). ABC transporters are a
subset of nucleotide hydrolases that contain a signature
motif, Q-loop, and H-loop/switch region, in addition to,
the Walker A motif/P-loop and Walker B motif commonly
found in a number of ATP- and GTP-binding and
hydrolyzing proteins.
Length = 171
Score = 31.6 bits (73), Expect = 0.37
Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 135 RFNAIIGPNGSGKSNVIDSMLFRF 158
AI+GP+GSGKS ++ +L R
Sbjct: 29 EKVAIVGPSGSGKSTLLK-LLLRL 51
Score = 30.0 bits (69), Expect = 1.4
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 157 RFNAIIGPNGSGKS 170
AI+GP+GSGKS
Sbjct: 29 EKVAIVGPSGSGKS 42
>gnl|CDD|213220 cd03253, ABCC_ATM1_transporter, ATP-binding cassette domain of
iron-sulfur clusters transporter, subfamily C. ATM1 is
an ABC transporter that is expressed in the
mitochondria. Although the specific function of ATM1 is
unknown, its disruption results in the accumulation of
excess mitochondrial iron, loss of mitochondrial
cytochromes, oxidative damage to mitochondrial DNA, and
decreased levels of cytosolic heme proteins. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 236
Score = 31.8 bits (73), Expect = 0.42
Identities = 13/21 (61%), Positives = 18/21 (85%), Gaps = 1/21 (4%)
Query: 138 AIIGPNGSGKSNVIDSMLFRF 158
AI+GP+GSGKS ++ +LFRF
Sbjct: 31 AIVGPSGSGKSTIL-RLLFRF 50
>gnl|CDD|172200 PRK13652, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 277
Score = 32.1 bits (73), Expect = 0.43
Identities = 18/33 (54%), Positives = 21/33 (63%), Gaps = 7/33 (21%)
Query: 138 AIIGPNGSGKSNVIDSMLFR-FNAIIGPNGSGK 169
A+IGPNG+GKS LFR FN I+ P SG
Sbjct: 34 AVIGPNGAGKST-----LFRHFNGILKPT-SGS 60
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form (CCALD),
the milder adult form, adrenomyeloneuropathy (AMN), and
variants without neurologic involvement (i.e.
asymptomatic).
Length = 166
Score = 31.4 bits (72), Expect = 0.44
Identities = 26/73 (35%), Positives = 36/73 (49%), Gaps = 21/73 (28%)
Query: 101 EVEQISMMPPKGKTEKETGLLEYLEEII--GTNRYKRFNAIIGPNGSGKSNVIDSMLFRF 158
E+E +S+ P G+ LL+ L I G I GP+G+GKS+ LFR
Sbjct: 2 ELENLSLATPDGRV-----LLKDLSFEIKPGDRLL-----ITGPSGTGKSS-----LFR- 45
Query: 159 NAIIG--PNGSGK 169
A+ G P GSG+
Sbjct: 46 -ALAGLWPWGSGR 57
>gnl|CDD|221957 pfam13175, AAA_15, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 320
Score = 32.0 bits (73), Expect = 0.48
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 159 NAIIGPNGSGKSNVIDSMLFVFGYRASKI 187
N IIG NGSGK+ +++++ + + I
Sbjct: 25 NVIIGENGSGKTTILEALDNLKEKKKIYI 53
Score = 29.3 bits (66), Expect = 3.3
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 137 NAIIGPNGSGKSNVIDSMLFRFN 159
N IIG NGSGK+ +++++
Sbjct: 25 NVIIGENGSGKTTILEALDNLKE 47
>gnl|CDD|143192 cd05715, Ig_P0-like, Immunoglobulin (Ig)-like domain of Protein
zero (P0) and similar proteins. Ig_P0ex-like: domain
similar to the immunoglobulin (Ig) domain of Protein
zero (P0). P0 accounts for over 50% of the total protein
in peripheral nervous system (PNS) myelin. P0 is a
single-pass transmembrane glycoprotein with a highly
basic intracellular domain and an extracellular Ig
domain. The extracellular domain of P0 (P0-ED) is
similar to the Ig variable domain, carrying one acceptor
sequence for N-linked glycosylation. P0 plays a role in
membrane adhesion in the spiral wraps of the myelin
sheath. The intracellular domain is thought to mediate
membrane apposition of the cytoplasmic faces and may,
through electrostatic interactions, interact directly
with lipid headgroups. It is thought that homophilic
interactions of the P0 extracellular domain mediate
membrane juxtaposition in the extracellular space of PNS
myelin. This group also contains the Ig domain of Sodium
channel subunit beta-2 (SCN2B), and of epithelial V-like
antigen 1 (EVA). EVA, also known as myelin protein
zero-like 2, is an adhesion molecule, which may play a
role in structural organization of the thymus and early
lymphocyte development. SCN2B subunits play a role in
determining sodium channel density and function in
neurons,and in control of electrical excitability in
the brain.
Length = 116
Score = 30.4 bits (69), Expect = 0.58
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 29 DGNVQTNDKSLDEHDLDLDDEGGTYVGEVYIPP 61
GN D S+ H+L D GTY +V PP
Sbjct: 72 VGNPSRKDASIVIHNLQFTDN-GTYTCDVKNPP 103
>gnl|CDD|224116 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway)
[DNA replication, recombination, and repair].
Length = 363
Score = 31.8 bits (73), Expect = 0.59
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 135 RFNAIIGPNGSGKSNVI 151
N ++G NG GK+N++
Sbjct: 24 GVNVLVGENGQGKTNLL 40
Score = 31.8 bits (73), Expect = 0.59
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 157 RFNAIIGPNGSGKSNVI 173
N ++G NG GK+N++
Sbjct: 24 GVNVLVGENGQGKTNLL 40
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain I
of the ABC component of a cobalt transport family found
in bacteria, archaea, and eukaryota. The transition
metal cobalt is an essential component of many enzymes
and must be transported into cells in appropriate
amounts when needed. This ABC transport system of the
CbiMNQO family is involved in cobalt transport in
association with the cobalamin (vitamin B12)
biosynthetic pathways. Most of cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are encoded
by the conserved gene cluster cbiMNQO. Both the CbiM and
CbiQ proteins are integral cytoplasmic membrane
proteins, and the CbiO protein has the linker peptide
and the Walker A and B motifs commonly found in the
ATPase components of the ABC-type transport systems.
Length = 211
Score = 31.3 bits (72), Expect = 0.60
Identities = 15/30 (50%), Positives = 18/30 (60%), Gaps = 6/30 (20%)
Query: 136 FNAIIGPNGSGKSNVIDSMLFR-FNAIIGP 164
F I+GPNGSGKS L R N ++GP
Sbjct: 29 FVLIVGPNGSGKST-----LLRLLNGLLGP 53
Score = 30.9 bits (71), Expect = 0.92
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 158 FNAIIGPNGSGKS 170
F I+GPNGSGKS
Sbjct: 29 FVLIVGPNGSGKS 41
>gnl|CDD|213180 cd03213, ABCG_EPDR, Eye pigment and drug resistance transporter
subfamily G of the ATP-binding cassette superfamily.
ABCG transporters are involved in eye pigment (EP)
precursor transport, regulation of lipid-trafficking
mechanisms, and pleiotropic drug resistance (DR). DR is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. Compared to other members of the
ABC transporter subfamilies, the ABCG transporter family
is composed of proteins that have an ATP-binding
cassette domain at the N-terminus and a TM
(transmembrane) domain at the C-terminus.
Length = 194
Score = 31.0 bits (71), Expect = 0.69
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 7/40 (17%)
Query: 124 LEEIIGTNRYKRFNAIIGPNGSGKSNVIDSMLFRFNAIIG 163
L+ + G + AI+GP+G+GKS ++L NA+ G
Sbjct: 25 LKNVSGKAKPGELTAIMGPSGAGKS----TLL---NALAG 57
Score = 29.8 bits (68), Expect = 1.8
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 157 RFNAIIGPNGSGKSNVID 174
AI+GP+G+GKS +++
Sbjct: 36 ELTAIMGPSGAGKSTLLN 53
>gnl|CDD|226648 COG4185, COG4185, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 187
Score = 30.9 bits (70), Expect = 0.70
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 134 KRFNAIIGPNGSGKSNVIDSMLFRFN 159
KR + + GPNGSGKS V S L
Sbjct: 2 KRLDIVAGPNGSGKSTVYASTLAPLL 27
>gnl|CDD|200134 TIGR01842, type_I_sec_PrtD, type I secretion system ABC
transporter, PrtD family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion [Protein fate, Protein and
peptide secretion and trafficking].
Length = 544
Score = 31.5 bits (72), Expect = 0.78
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 11/50 (22%)
Query: 101 EVEQISMMPPKGKTEKETGLLEYLE--EIIGTNRYKRFNAIIGPNGSGKS 148
VE ++++PP GK G+ L+ E + AIIGP+GSGKS
Sbjct: 318 SVENVTIVPPGGKKPTLRGISFSLQAGEAL---------AIIGPSGSGKS 358
Score = 31.5 bits (72), Expect = 0.79
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 137 NAIIGPNGSGKSNVIDSMLFRFNA-----IIGPNGSGKSNVIDSMLFVFGYRASKIR 188
N I P G GK + + F A IIGP+GSGKS + ++ ++ + +R
Sbjct: 321 NVTIVPPG-GKKPTLRGISFSLQAGEALAIIGPSGSGKSTLARLIVGIWPPTSGSVR 376
>gnl|CDD|223488 COG0411, LivG, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 250
Score = 31.0 bits (71), Expect = 0.81
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 7/26 (26%)
Query: 138 AIIGPNGSGKSNVIDSMLFRFNAIIG 163
+IGPNG+GK+ + FN I G
Sbjct: 34 GLIGPNGAGKTTL-------FNLITG 52
Score = 31.0 bits (71), Expect = 0.83
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 160 AIIGPNGSGKSNVID 174
+IGPNG+GK+ + +
Sbjct: 34 GLIGPNGAGKTTLFN 48
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 31.0 bits (71), Expect = 0.86
Identities = 9/24 (37%), Positives = 18/24 (75%)
Query: 138 AIIGPNGSGKSNVIDSMLFRFNAI 161
A++G +GSGK+ + +++L+ AI
Sbjct: 3 ALVGHSGSGKTTLAEALLYATGAI 26
Score = 30.6 bits (70), Expect = 1.2
Identities = 8/22 (36%), Positives = 17/22 (77%)
Query: 160 AIIGPNGSGKSNVIDSMLFVFG 181
A++G +GSGK+ + +++L+ G
Sbjct: 3 ALVGHSGSGKTTLAEALLYATG 24
>gnl|CDD|238661 cd01365, KISc_KIF1A_KIF1B, Kinesin motor domain, KIF1_like
proteins. KIF1A (Unc104) transports synaptic vesicles to
the nerve terminal, KIF1B has been implicated in
transport of mitochondria. Both proteins are expressed
in neurons. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
In contrast to the majority of dimeric kinesins, most
KIF1A/Unc104 kinesins are monomeric motors. A
lysine-rich loop in KIF1A binds to the negatively
charged C-terminus of tubulin and compensates for the
lack of a second motor domain, allowing KIF1A to move
processively.
Length = 356
Score = 31.1 bits (71), Expect = 0.96
Identities = 14/70 (20%), Positives = 30/70 (42%), Gaps = 5/70 (7%)
Query: 206 SRCSVAIHFAQIIDKPNEEYEIIPGTDLEIARTAFYDNSSYYTLNGKKVHFKEVAKVLRD 265
S+C V + K + + + ++ +D SY++ + + H+ V D
Sbjct: 21 SKCIVQMPGKVTTLKNPKAADATR----KKPKSFSFD-HSYWSHDSEDPHYASQEDVFED 75
Query: 266 HGVDLLNNRF 275
G +LL++ F
Sbjct: 76 LGRELLDHAF 85
>gnl|CDD|234200 TIGR03411, urea_trans_UrtD, urea ABC transporter, ATP-binding
protein UrtD. Members of this protein family are ABC
transporter ATP-binding subunits associated with urea
transport and metabolism. This protein is found in a
conserved five-gene transport operon typically found
adjacent to urease genes. It was shown in Cyanobacteria
that disruption leads to the loss of high-affinity urea
transport activity [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 242
Score = 30.6 bits (70), Expect = 1.0
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 138 AIIGPNGSGKSNVID 152
IIGPNG+GK+ ++D
Sbjct: 32 VIIGPNGAGKTTMMD 46
Score = 30.6 bits (70), Expect = 1.0
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 160 AIIGPNGSGKSNVID 174
IIGPNG+GK+ ++D
Sbjct: 32 VIIGPNGAGKTTMMD 46
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 31.1 bits (71), Expect = 1.1
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 160 AIIGPNGSGKSNVIDSMLFVFGYRASKIRANKLSV 194
AI+G +GSGKS ++ + + + I N + +
Sbjct: 368 AILGRSGSGKSTLLQLLAGAWDPQQGSITLNGVEI 402
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 31.2 bits (71), Expect = 1.1
Identities = 35/129 (27%), Positives = 59/129 (45%), Gaps = 19/129 (14%)
Query: 278 LQEPIAKMEVLYGKYDEERTEKLTRVQLVETDLKALEPELRKAVNFL-ELENCVQRKHNE 336
L+E + ++E Y +Y E + + ++ E +LK LE EL KA L E E ++ E
Sbjct: 590 LEERLKELEPFYNEYLELKDAE-KELEREEKELKKLEEELDKAFEELAETEKRLEELRKE 648
Query: 337 I------YQYERYVNMKNL-----GEHETKVQQME------QELTANLESIKKCTDEMES 379
+ Y E Y ++ E ++E +E+ LE +K+ +E E
Sbjct: 649 LEELEKKYSEEEYEELREEYLELSRELAGLRAELEELEKRREEIKKTLEKLKEELEEREK 708
Query: 380 AKTELKTVE 388
AK EL+ +E
Sbjct: 709 AKKELEKLE 717
Score = 29.6 bits (67), Expect = 3.4
Identities = 11/19 (57%), Positives = 17/19 (89%)
Query: 137 NAIIGPNGSGKSNVIDSML 155
N IIG NGSGKS++++++L
Sbjct: 26 NLIIGQNGSGKSSILEAIL 44
Score = 29.6 bits (67), Expect = 3.4
Identities = 11/19 (57%), Positives = 17/19 (89%)
Query: 159 NAIIGPNGSGKSNVIDSML 177
N IIG NGSGKS++++++L
Sbjct: 26 NLIIGQNGSGKSSILEAIL 44
Score = 28.5 bits (64), Expect = 7.3
Identities = 31/148 (20%), Positives = 71/148 (47%), Gaps = 19/148 (12%)
Query: 257 KEVAKVLRDHGVDLLNNRFLILQEPIAKMEVLYGKYDEER---TEKLTRVQLVETDLKAL 313
KE+ +VLR+ ++ +++ L+E + K+E + +E + E ++ +E + L
Sbjct: 200 KELEEVLRE--INEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKL 257
Query: 314 EP---ELRKAVNFL-----ELENCVQRKHNEIYQY-ERYVNMKNL-GEHETKVQQMEQEL 363
E EL + + L ELE V+ E+ + E Y+ + E+ +++++E+ L
Sbjct: 258 EEKIRELEERIEELKKEIEELEEKVKEL-KELKEKAEEYIKLSEFYEEYLDELREIEKRL 316
Query: 364 ---TANLESIKKCTDEMESAKTELKTVE 388
+ I++ E+E + L+ ++
Sbjct: 317 SRLEEEINGIEERIKELEEKEERLEELK 344
>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 30.8 bits (70), Expect = 1.1
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 5/32 (15%)
Query: 144 GSGKSNVIDSMLFRF-----NAIIGPNGSGKS 170
G G +++ + A+IGPNG GKS
Sbjct: 11 GYGTKRILNDLSLSLPTGKITALIGPNGCGKS 42
Score = 27.7 bits (62), Expect = 9.1
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 138 AIIGPNGSGKS 148
A+IGPNG GKS
Sbjct: 32 ALIGPNGCGKS 42
>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 = 30.8 bits (70), Expect = 1.2
Identities = 10/21 (47%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 138 AIIGPNGSGKSNVIDSMLFRF 158
A++GP+G+GKS + +L RF
Sbjct: 370 ALVGPSGAGKSTLF-QLLLRF 389
>gnl|CDD|223473 COG0396, sufC, Cysteine desulfurase activator ATPase
[Posttranslational modification, protein turnover,
chaperones].
Length = 251
Score = 30.6 bits (70), Expect = 1.2
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 136 FNAIIGPNGSGKS 148
+AI+GPNGSGKS
Sbjct: 32 VHAIMGPNGSGKS 44
Score = 30.6 bits (70), Expect = 1.2
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 158 FNAIIGPNGSGKS 170
+AI+GPNGSGKS
Sbjct: 32 VHAIMGPNGSGKS 44
>gnl|CDD|235150 PRK03695, PRK03695, vitamin B12-transporter ATPase; Provisional.
Length = 248
Score = 30.3 bits (69), Expect = 1.3
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 139 IIGPNGSGKSNVIDSM 154
++GPNG+GKS ++ M
Sbjct: 27 LVGPNGAGKSTLLARM 42
Score = 30.3 bits (69), Expect = 1.3
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 161 IIGPNGSGKSNVIDSM 176
++GPNG+GKS ++ M
Sbjct: 27 LVGPNGAGKSTLLARM 42
>gnl|CDD|114591 pfam05873, Mt_ATP-synt_D, ATP synthase D chain, mitochondrial
(ATP5H). This family consists of several ATP synthase D
chain, mitochondrial (ATP5H) proteins. Subunit d has no
extensive hydrophobic sequences, and is not apparently
related to any subunit described in the simpler ATP
synthases in bacteria and chloroplasts.
Length = 160
Score = 29.8 bits (67), Expect = 1.3
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 12/68 (17%)
Query: 317 LRKAVNFLELENCVQRKHNEI---YQYERY---------VNMKNLGEHETKVQQMEQELT 364
+K V L + ++K+ + Y ++Y ++K + E++TK QE
Sbjct: 56 YKKNVPKAGLVDSFEKKYEALKVPYPEDKYTAQVDAEEKEDVKRIAEYKTKSADRIQEYE 115
Query: 365 ANLESIKK 372
LE K
Sbjct: 116 KELEKWKN 123
>gnl|CDD|217619 pfam03571, Peptidase_M49, Peptidase family M49.
Length = 550
Score = 30.7 bits (70), Expect = 1.3
Identities = 25/122 (20%), Positives = 42/122 (34%), Gaps = 19/122 (15%)
Query: 244 SSYYTLNGKKVHFKEVAKVLRDHGVDLLNNR--------FLILQEPIAKMEVLYGKYDEE 295
S+YY+ N K + + L+ + N R + +L + E +
Sbjct: 28 STYYSGNITKEEAELINDFLKSKNIMPENTRVFKHGDGVYEVLVASVEVSEK-TEPEGPD 86
Query: 296 RTEKLTRVQLVETDLKALEPELRKAVNFLEL-----ENCVQRKHNEIYQYERYVNMKNLG 350
+V++ D PEL+K V LE N QRK + Y ++
Sbjct: 87 TEYNGKKVKVTRGDHS---PELKKVVEHLEKAKKYAANDNQRKM--LEYYIESFTTGSIE 141
Query: 351 EH 352
H
Sbjct: 142 AH 143
>gnl|CDD|233065 TIGR00634, recN, DNA repair protein RecN. All proteins in this
family for which functions are known are ATP binding
proteins involved in the initiation of recombination and
recombinational repair [DNA metabolism, DNA replication,
recombination, and repair].
Length = 563
Score = 30.9 bits (70), Expect = 1.5
Identities = 46/231 (19%), Positives = 86/231 (37%), Gaps = 41/231 (17%)
Query: 158 FNAIIGPNGSGKSNVIDSMLFVFGYRASKIRANKLSVLMHKSDQVGGVSRCSVAIHFAQI 217
+ G G+GKS +ID++ + G RA R G +R V F
Sbjct: 24 LTVLTGETGAGKSMIIDALSLLGGQRAGASRVRS------------GENRAVVEGRF-TT 70
Query: 218 IDKPNEEYEIIPGTDLE---------IARTAFYDNSSYYTLNGKKVHFKEVAKVLRD--- 265
+ +Y + +LE + R+ D S LNGK V + + +
Sbjct: 71 ESLDDADYPALQAIELEEEDEDGEVILRRSISRDGRSRAYLNGKPVSASSLLEFTSELLD 130
Query: 266 -HGVDLLNNRFLILQEPIAKMEVL--YGKYDEERTEKLTRVQLVETDLKALEPELRKAVN 322
HG + +L P + ++L + +E+ V+ +A ++ +
Sbjct: 131 LHG----QHDQQLLFRPDEQRQLLDTFAGANEK-------VKAYRELYQAWLKARQQLKD 179
Query: 323 FLELE-NCVQRKHNEIYQYERYVNMKNLGEHETKVQQMEQELTANLESIKK 372
+ E QR +Q E + +L E + + EQ+ +NLE +++
Sbjct: 180 RQQKEQELAQRLDFLQFQLEE-LEEADLQPGEDEALEAEQQRLSNLEKLRE 229
>gnl|CDD|217843 pfam04012, PspA_IM30, PspA/IM30 family. This family includes PspA
a protein that suppresses sigma54-dependent
transcription. The PspA protein, a negative regulator of
the Escherichia coli phage shock psp operon, is produced
when virulence factors are exported through secretins in
many Gram-negative pathogenic bacteria and its homologue
in plants, VIPP1, plays a critical role in thylakoid
biogenesis, essential for photosynthesis. Activation of
transcription by the enhancer-dependent bacterial
sigma(54) containing RNA polymerase occurs through ATP
hydrolysis-driven protein conformational changes enabled
by activator proteins that belong to the large AAA(+)
mechanochemical protein family. It has been shown that
PspA directly and specifically acts upon and binds to
the AAA(+) domain of the PspF transcription activator.
Length = 220
Score = 30.0 bits (68), Expect = 1.5
Identities = 32/144 (22%), Positives = 59/144 (40%), Gaps = 28/144 (19%)
Query: 256 FKEVAKVLR---DHGVDLLNNRFLILQEPIAKMEVLYGKYDEERTEKLTRVQLVETDLKA 312
FK + ++LR G+D + +L++ I M+ GK + + + R + +E L+
Sbjct: 3 FKRLLRLLRANIHEGLDKAEDPEKMLEQAIRDMQSELGKARQALAQVIARQKQLERKLEE 62
Query: 313 LEPELRK----------------AVNFLE----LENCVQRKHNEIYQYERYVN--MKNLG 350
+ + +K A L LE + ++ Q V K L
Sbjct: 63 QKEQAKKLENKARAALTKGNEELAREALAEIATLEKQAEALETQLTQQRSAVEQLRKQLA 122
Query: 351 EHETKVQQMEQELT---ANLESIK 371
ETK+QQ++ + T A L++ K
Sbjct: 123 ALETKIQQLKAKKTALKARLKAAK 146
>gnl|CDD|190201 pfam02058, Guanylin, Guanylin precursor.
Length = 87
Score = 28.5 bits (64), Expect = 1.6
Identities = 8/28 (28%), Positives = 12/28 (42%)
Query: 356 VQQMEQELTANLESIKKCTDEMESAKTE 383
V + + +LES+KK D E
Sbjct: 1 VTVQDGGFSFSLESVKKLKDLQEQWAQS 28
>gnl|CDD|233206 TIGR00954, 3a01203, Peroxysomal Fatty Acyl CoA Transporter (FAT)
Family protei. [Transport and binding proteins,
Carbohydrates, organic alcohols, and acids].
Length = 659
Score = 30.5 bits (69), Expect = 1.6
Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 19/103 (18%)
Query: 100 GEVEQISMMPPKGKTEKETGLLEYLEEIIGTNRYKRFNAI--IGPNGSGKSNVIDSMLFR 157
E+E G++EY + I +F I + PNG +I+S+ F
Sbjct: 424 EEIESGREGGRNSNLVPGRGIVEYQDNGI------KFENIPLVTPNGD---VLIESLSFE 474
Query: 158 FNA-----IIGPNGSGKSN---VIDSMLFVFGYRASKIRANKL 192
+ I GPNG GKS+ ++ + V+G R +K KL
Sbjct: 475 VPSGNNLLICGPNGCGKSSLFRILGELWPVYGGRLTKPAKGKL 517
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 30.3 bits (69), Expect = 1.6
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 138 AIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGKSNV 172
A++GP+G+GKS ++ ++L F G V
Sbjct: 352 ALVGPSGAGKSTLL-NLLLGF----VDPTEGSIAV 381
Score = 29.6 bits (67), Expect = 3.7
Identities = 10/37 (27%), Positives = 21/37 (56%), Gaps = 5/37 (13%)
Query: 146 GKSNVIDSMLFRFN-----AIIGPNGSGKSNVIDSML 177
G+ + + F A++GP+G+GKS +++ +L
Sbjct: 333 GRRPALRPVSFTVPPGERVALVGPSGAGKSTLLNLLL 369
>gnl|CDD|182336 PRK10253, PRK10253, iron-enterobactin transporter ATP-binding
protein; Provisional.
Length = 265
Score = 30.3 bits (68), Expect = 1.7
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 136 FNAIIGPNGSGKSNVIDSM 154
F AIIGPNG GKS ++ ++
Sbjct: 35 FTAIIGPNGCGKSTLLRTL 53
Score = 30.3 bits (68), Expect = 1.7
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 158 FNAIIGPNGSGKSNVIDSM 176
F AIIGPNG GKS ++ ++
Sbjct: 35 FTAIIGPNGCGKSTLLRTL 53
>gnl|CDD|213227 cd03260, ABC_PstB_phosphate_transporter, ATP-binding cassette
domain of the phosphate transport system. Phosphate
uptake is of fundamental importance in the cell
physiology of bacteria because phosphate is required as
a nutrient. The Pst system of E. coli comprises four
distinct subunits encoded by the pstS, pstA, pstB, and
pstC genes. The PstS protein is a phosphate-binding
protein located in the periplasmic space. PstA and PstC
are hydrophobic and they form the transmembrane portion
of the Pst system. PstB is the catalytic subunit, which
couples the energy of ATP hydrolysis to the import of
phosphate across cellular membranes through the Pst
system, often referred as ABC-protein. PstB belongs to
one of the largest superfamilies of proteins
characterized by a highly conserved adenosine
triphosphate (ATP) binding cassette (ABC), which is also
a nucleotide binding domain (NBD).
Length = 227
Score = 29.8 bits (68), Expect = 1.7
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 138 AIIGPNGSGKS 148
A+IGP+G GKS
Sbjct: 30 ALIGPSGCGKS 40
Score = 29.8 bits (68), Expect = 1.7
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 160 AIIGPNGSGKS 170
A+IGP+G GKS
Sbjct: 30 ALIGPSGCGKS 40
>gnl|CDD|237457 PRK13647, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 274
Score = 30.1 bits (68), Expect = 1.7
Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 4/24 (16%)
Query: 138 AIIGPNGSGKSNVIDSMLFRFNAI 161
A++GPNG+GKS ++L N I
Sbjct: 35 ALLGPNGAGKS----TLLLHLNGI 54
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 30.4 bits (69), Expect = 1.8
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 134 KRFNAIIGPNGSGKSNVIDSMLFR 157
K+ N I G NGSGK+ + S LFR
Sbjct: 16 KKVNLIYGRNGSGKTTL--SRLFR 37
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 29.9 bits (68), Expect = 2.0
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 136 FNAIIGPNGSGKS 148
+IGPNGSGKS
Sbjct: 32 RVLLIGPNGSGKS 44
Score = 29.9 bits (68), Expect = 2.0
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 158 FNAIIGPNGSGKS 170
+IGPNGSGKS
Sbjct: 32 RVLLIGPNGSGKS 44
>gnl|CDD|183080 PRK11300, livG, leucine/isoleucine/valine transporter ATP-binding
subunit; Provisional.
Length = 255
Score = 30.0 bits (68), Expect = 2.1
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 7/26 (26%)
Query: 138 AIIGPNGSGKSNVIDSMLFRFNAIIG 163
++IGPNG+GK+ V FN + G
Sbjct: 35 SLIGPNGAGKTTV-------FNCLTG 53
Score = 28.4 bits (64), Expect = 5.8
Identities = 8/13 (61%), Positives = 12/13 (92%)
Query: 160 AIIGPNGSGKSNV 172
++IGPNG+GK+ V
Sbjct: 35 SLIGPNGAGKTTV 47
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA ternary
complex to the ribosomal A site by facilitated release
of the deacylated tRNA from the E site. The reaction
requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 29.0 bits (66), Expect = 2.2
Identities = 6/11 (54%), Positives = 9/11 (81%)
Query: 138 AIIGPNGSGKS 148
++G NG+GKS
Sbjct: 30 GLVGRNGAGKS 40
Score = 29.0 bits (66), Expect = 2.2
Identities = 6/11 (54%), Positives = 9/11 (81%)
Query: 160 AIIGPNGSGKS 170
++G NG+GKS
Sbjct: 30 GLVGRNGAGKS 40
>gnl|CDD|213223 cd03256, ABC_PhnC_transporter, ATP-binding cassette domain of the
binding protein-dependent phosphonate transport system.
Phosphonates are a class of organophosphorus compounds
characterized by a chemically stable
carbon-to-phosphorus (C-P) bond. Phosphonates are
widespread among naturally occurring compounds in all
kingdoms of wildlife, but only prokaryotic
microorganisms are able to cleave this bond. Certain
bacteria such as E. coli can use alkylphosphonates as a
phosphorus source. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 241
Score = 29.8 bits (68), Expect = 2.2
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 5/40 (12%)
Query: 136 FNAIIGPNGSGKSNVIDSMLFRFNAIIGP-NGSGKSNVID 174
F A+IGP+G+GKS ++L N ++ P +GS + D
Sbjct: 29 FVALIGPSGAGKS----TLLRCLNGLVEPTSGSVLIDGTD 64
>gnl|CDD|226359 COG3839, MalK, ABC-type sugar transport systems, ATPase components
[Carbohydrate transport and metabolism].
Length = 338
Score = 29.9 bits (68), Expect = 2.3
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 134 KRFNAIIGPNGSGKS 148
F ++GP+G GKS
Sbjct: 29 GEFVVLLGPSGCGKS 43
Score = 29.9 bits (68), Expect = 2.3
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 158 FNAIIGPNGSGKS 170
F ++GP+G GKS
Sbjct: 31 FVVLLGPSGCGKS 43
>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572). Family of
eukaryotic proteins with undetermined function.
Length = 321
Score = 29.7 bits (67), Expect = 2.3
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 346 MKNLGEHETKVQQMEQELTANLESIKK 372
MK L E+ T + E E+ LE +K+
Sbjct: 134 MKKL-ENRTADSKREMEVLERLEELKE 159
>gnl|CDD|213221 cd03254, ABCC_Glucan_exporter_like, ATP-binding cassette domain of
glucan transporter and related proteins, subfamily C.
Glucan exporter ATP-binding protein. In A. tumefaciens
cyclic beta-1, 2-glucan must be transported into the
periplasmic space to exert its action as a virulence
factor. This subfamily belongs to the MRP-like family
and is involved in drug, peptide, and lipid export. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains each composed of six
transmembrane (TM) helices and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 229
Score = 29.5 bits (67), Expect = 2.4
Identities = 11/21 (52%), Positives = 17/21 (80%), Gaps = 1/21 (4%)
Query: 138 AIIGPNGSGKSNVIDSMLFRF 158
AI+GP G+GK+ +I ++L RF
Sbjct: 33 AIVGPTGAGKTTLI-NLLMRF 52
Score = 28.0 bits (63), Expect = 8.4
Identities = 8/14 (57%), Positives = 12/14 (85%)
Query: 160 AIIGPNGSGKSNVI 173
AI+GP G+GK+ +I
Sbjct: 33 AIVGPTGAGKTTLI 46
>gnl|CDD|213187 cd03220, ABC_KpsT_Wzt, ATP-binding cassette component of
polysaccharide transport system. The KpsT/Wzt ABC
transporter subfamily is involved in extracellular
polysaccharide export. Among the variety of
membrane-linked or extracellular polysaccharides
excreted by bacteria, only capsular polysaccharides,
lipopolysaccharides, and teichoic acids have been shown
to be exported by ABC transporters. A typical system is
made of a conserved integral membrane and an ABC. In
addition to these proteins, capsular polysaccharide
exporter systems require two 'accessory' proteins to
perform their function: a periplasmic (E.coli) or a
lipid-anchored outer membrane protein called OMA
(Neisseria meningitidis and Haemophilus influenza) and a
cytoplasmic membrane protein MPA2.
Length = 224
Score = 29.4 bits (67), Expect = 2.4
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 5/47 (10%)
Query: 129 GTNRYKRFNAIIGPNGSGKSNVIDSMLFRFN-----AIIGPNGSGKS 170
G++ K+ + G+ + + F +IG NG+GKS
Sbjct: 16 GSSSLKKLGILGRKGEVGEFWALKDVSFEVPRGERIGLIGRNGAGKS 62
>gnl|CDD|213216 cd03249, ABC_MTABC3_MDL1_MDL2, ATP-binding cassette domain of a
mitochondrial protein MTABC3 and related proteins.
MTABC3 (also known as ABCB6) is a mitochondrial
ATP-binding cassette protein involved in iron
homeostasis and one of four ABC transporters expressed
in the mitochondrial inner membrane, the other three
being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast
MDL1 (multidrug resistance-like protein 1) and MDL2
(multidrug resistance-like protein 2) transporters are
also included in this CD. MDL1 is an ATP-dependent
permease that acts as a high-copy suppressor of ATM1 and
is thought to have a role in resistance to oxidative
stress. Interestingly, subfamily B is more closely
related to the carboxyl-terminal component of subfamily
C than the two halves of ABCC molecules are with one
another.
Length = 238
Score = 29.4 bits (67), Expect = 2.4
Identities = 11/21 (52%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 138 AIIGPNGSGKSNVIDSMLFRF 158
A++G +G GKS V+ S+L RF
Sbjct: 33 ALVGSSGCGKSTVV-SLLERF 52
>gnl|CDD|219866 pfam08494, DEAD_assoc, DEAD/H associated. This domain is found in
ATP-dependent helicases as well as a number of
hypothetical proteins together with the helicase
conserved C-terminal domain (pfam00270) and the
pfam00271 domain.
Length = 188
Score = 29.4 bits (67), Expect = 2.5
Identities = 24/85 (28%), Positives = 35/85 (41%), Gaps = 25/85 (29%)
Query: 253 KVHFKEVAK----VLRDHGV-------------DLLNNR-----FLILQEPIAKMEVLYG 290
K F+EVA+ +LR + LL+ R +L+E A E L
Sbjct: 99 KRRFREVARRAGLILRRYPGKRKSLRQQRISSDLLLDLRKYYPDHPLLKE--ALREALED 156
Query: 291 KYDEERTEK-LTRVQLVETDLKALE 314
D ER E+ L R++ E + LE
Sbjct: 157 YLDVERLEELLERIREGEIRVVELE 181
>gnl|CDD|213184 cd03217, ABC_FeS_Assembly, ABC-type transport system involved in
Fe-S cluster assembly, ATPase component. Biosynthesis
of iron-sulfur clusters (Fe-S) depends on multi-protein
systems. The SUF system of E. coli and Erwinia
chrysanthemi is important for Fe-S biogenesis under
stressful conditions. The SUF system is made of six
proteins: SufC is an atypical cytoplasmic ABC-ATPase,
which forms a complex with SufB and SufD; SufA plays the
role of a scaffold protein for assembly of iron-sulfur
clusters and delivery to target proteins; SufS is a
cysteine desulfurase which mobilizes the sulfur atom
from cysteine and provides it to the cluster; SufE has
no associated function yet.
Length = 200
Score = 29.0 bits (66), Expect = 2.8
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 136 FNAIIGPNGSGKS 148
+A++GPNGSGKS
Sbjct: 28 VHALMGPNGSGKS 40
Score = 29.0 bits (66), Expect = 2.8
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 158 FNAIIGPNGSGKS 170
+A++GPNGSGKS
Sbjct: 28 VHALMGPNGSGKS 40
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 28.4 bits (64), Expect = 2.8
Identities = 12/66 (18%), Positives = 25/66 (37%), Gaps = 5/66 (7%)
Query: 132 RYKRFNAIIGPNGSGKSNVIDSML-----FRFNAIIGPNGSGKSNVIDSMLFVFGYRASK 186
R + G +GSGK+ ++ + R + P+ +++ +L G S
Sbjct: 2 RGAGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSG 61
Query: 187 IRANKL 192
+L
Sbjct: 62 GTTAEL 67
>gnl|CDD|148674 pfam07212, Hyaluronidase_1, Hyaluronidase protein (HylP). This
family consists of several phage associated
hyaluronidase proteins (EC:3.2.1.35) which seem to be
specific to Streptococcus pyogenes and Streptococcus
pyogenes bacteriophages. The substrate of hyaluronidase
is hyaluronic acid, a sugar polymer composed of
alternating N-acetylglucosamine and glucuronic acid
residues. Hyaluronic acid is found in the ground
substance of human connective tissue and the vitreous
of the eye and also is the sole component of the
capsule of group A streptococci. The capsule has been
shown to be an important virulence factor of this
organism by virtue of its ability to resist
phagocytosis. Production by S. pyogenes of both a
hyaluronic acid capsule and hyaluronidase enzymatic
activity capable of destroying the capsule is an
interesting, yet-unexplained, phenomenon.
Length = 273
Score = 29.6 bits (66), Expect = 2.8
Identities = 22/65 (33%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 10 PNQDTLVTPKR--AKKTQEQDDGNVQTNDKSLDEHDLDLDDEGGTYVGEVYIPPIAPVCF 67
PN D L T K Q+ D V T +S E D L+ +GG G++ P A V +
Sbjct: 3 PNIDALATKVETAQKLQQKADKETVYTKAESKQELDKKLNLKGGVMTGQLKFKPAATVAY 62
Query: 68 ADPTG 72
+ TG
Sbjct: 63 SSSTG 67
>gnl|CDD|205039 pfam12718, Tropomyosin_1, Tropomyosin like. This family is a set
of eukaryotic tropomyosins. Within the yeast Tmp1 and
Tmp2, biochemical and sequence analyses indicate that
Tpm2p spans four actin monomers along a filament,
whereas Tpmlp spans five. Despite its shorter length,
Tpm2p can compete with Tpm1p for binding to F-actin.
Over-expression of Tpm2p in vivo alters the axial
budding of haploids to a bipolar pattern, and this can
be partially suppressed by co-over-expression of Tpm1p.
This suggests distinct functions for the two
tropomyosins, and indicates that the ratio between them
is important for correct morphogenesis. The family also
contains higher eukaryote Tmp3 members.
Length = 143
Score = 28.7 bits (65), Expect = 2.9
Identities = 19/90 (21%), Positives = 43/90 (47%), Gaps = 15/90 (16%)
Query: 291 KYDEERTEKLTRVQLVETDLKALEPELRKAVNFLELENCVQRKHNEIYQYERYVNMKNLG 350
+ ++E T + Q +E +++ LE +L++A LE E+ + E
Sbjct: 32 EKEQEITSLQKKNQQLEEEVEKLEEQLKEAKEKLE-ESEKLATNAEALT----------- 79
Query: 351 EHETKVQQMEQELTANLESIKKCTDEMESA 380
++Q +E+EL + + +K+ T+++ A
Sbjct: 80 ---RRIQLLEEELEESEKRLKETTEKLREA 106
>gnl|CDD|183662 PRK12662, PRK12662, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 492
Score = 29.7 bits (67), Expect = 3.1
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 268 VDLLNNRFLILQEPIAKMEVLYGKYDEER 296
VD+L+ L+L IA M VLYG Y +
Sbjct: 74 VDILSATMLVLVNFIAVMSVLYGIYPNRK 102
>gnl|CDD|224059 COG1136, SalX, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 226
Score = 29.0 bits (66), Expect = 3.3
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 10/46 (21%)
Query: 158 FNAIIGPNGSGKS---NVIDSML-------FVFGYRASKIRANKLS 193
F AI+GP+GSGKS N++ + + G +K+ +L+
Sbjct: 33 FVAIVGPSGSGKSTLLNLLGGLDKPTSGEVLINGKDLTKLSEKELA 78
Score = 29.0 bits (66), Expect = 3.4
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 136 FNAIIGPNGSGKS 148
F AI+GP+GSGKS
Sbjct: 33 FVAIVGPSGSGKS 45
>gnl|CDD|184199 PRK13639, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 275
Score = 29.3 bits (66), Expect = 3.5
Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 5/32 (15%)
Query: 138 AIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGK 169
A++GPNG+GKS ++ FN I+ P SG+
Sbjct: 32 ALLGPNGAGKS----TLFLHFNGILKPT-SGE 58
>gnl|CDD|237421 PRK13539, PRK13539, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 207
Score = 29.1 bits (66), Expect = 3.6
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 138 AIIGPNGSGKS 148
+ GPNGSGK+
Sbjct: 32 VLTGPNGSGKT 42
Score = 29.1 bits (66), Expect = 3.6
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 160 AIIGPNGSGKS 170
+ GPNGSGK+
Sbjct: 32 VLTGPNGSGKT 42
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 29.5 bits (66), Expect = 3.6
Identities = 43/242 (17%), Positives = 80/242 (33%), Gaps = 40/242 (16%)
Query: 159 NAIIGPNGSGKSNVIDSMLFVFGYRASKIRANKLSVLMHKSDQVGGVSRCSVAIHF---- 214
N I G NG+GKS+++D++ F + R K+ ++ K G + V + F
Sbjct: 26 NIITGKNGAGKSSIVDAIRFAL---FTDKRTEKIEDMIKK-----GKNNLEVELEFRIGG 77
Query: 215 -AQIIDKPNEEYEIIPGTDLEIARTAFYDNSSYYTLNGKKVHFKEVAKVLRDHGVDLLNN 273
I + E + I + + S K + K + D+ N
Sbjct: 78 HVYQIRRSIERRGKGSRREAYIKK-----DGSIIAEGFDDTT-KYIEKNILGISKDVFLN 131
Query: 274 RFLILQEPIAKMEVLYGKYDEERTE---------KLTRVQLVETD-LKALEPELRKAVNF 323
+ Q +M+ L +R + L R D + L E+ N
Sbjct: 132 SIFVGQ---GEMDSLISGDPAQRKKILDEILEINSLERNYDKLKDVIDMLRAEIS---NI 185
Query: 324 LELENCVQRKHNEIYQYERYVNMKNLGEHETKVQQMEQELTANLESIKKCTDEMESAKTE 383
LE ++ + E+ K + + E +E+ D+ + K+
Sbjct: 186 DYLEEKLKSSNLELEN-----IKKQIADDEKSHSITLKEIERLSIEYNNAMDDYNNLKSA 240
Query: 384 LK 385
L
Sbjct: 241 LN 242
>gnl|CDD|226121 COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD
family [DNA replication, recombination, and repair].
Length = 581
Score = 29.3 bits (66), Expect = 3.7
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 159 NAIIGPNGSGKSNVIDSMLFVFG 181
N +IG N SGKS+++D++ +
Sbjct: 26 NVLIGENNSGKSSLLDALRLLLD 48
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 29.4 bits (67), Expect = 3.7
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 12/42 (28%)
Query: 131 NRYKRFNAIIGPNGS---GKSNVIDSMLFRFNAIIGPNGSGK 169
N YKR + KSN++ +IGP GSGK
Sbjct: 89 NHYKRLRHGDKKDDDVELQKSNIL---------LIGPTGSGK 121
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.4 bits (67), Expect = 3.8
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 325 ELENCVQRKHNEIYQYERYVNMK--NLGEHETKVQQMEQELTANLESIKKCTDEMESAKT 382
E E ++ + NE+ + E+ + K NL +++ E+EL + +++ E+E +
Sbjct: 72 EFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEE 131
Query: 383 ELKTVE 388
EL+ +
Sbjct: 132 ELEELI 137
>gnl|CDD|100023 cd06059, Tubulin, The tubulin superfamily includes five distinct
families, the alpha-, beta-, gamma-, delta-, and
epsilon-tubulins and a sixth family (zeta-tubulin) which
is present only in kinetoplastid protozoa. The alpha-
and beta-tubulins are the major components of
microtubules, while gamma-tubulin plays a major role in
the nucleation of microtubule assembly. The delta- and
epsilon-tubulins are widespread but unlike the alpha,
beta, and gamma-tubulins they are not ubiquitous among
eukaryotes. The alpha/beta-tubulin heterodimer is the
structural subunit of microtubules. The alpha- and
beta-tubulins share 40% amino-acid sequence identity,
exist in several isotype forms, and undergo a variety of
posttranslational modifications. The structures of
alpha- and beta-tubulin are basically identical: each
monomer is formed by a core of two beta-sheets
surrounded by alpha-helices. The monomer structure is
very compact, but can be divided into three regions
based on function: the amino-terminal nucleotide-binding
region, an intermediate taxol-binding region and the
carboxy-terminal region which probably constitutes the
binding surface for motor proteins. Also included in
this group is the mitochondrial Misato/DML1 protein
family, involved in mitochondrial fusion and in
mitochondrial distribution and morphology.
Length = 382
Score = 29.2 bits (66), Expect = 3.8
Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 17/74 (22%)
Query: 136 FNAIIGPNGSGKSNVIDSML-------FRFNAIIGPNGSGKSNVIDSMLFVFGYRASKIR 188
+++ G GSG +++ +L I P+ G SNV++ +
Sbjct: 95 THSLGGGTGSGLGSLLLELLSDEYPKILINTFSIFPSPQGSSNVVEPYNSILS------- 147
Query: 189 ANKLSVLMHKSDQV 202
L+ L+ SD V
Sbjct: 148 ---LNHLLENSDSV 158
>gnl|CDD|131368 TIGR02315, ABC_phnC, phosphonate ABC transporter, ATP-binding
protein. Phosphonates are a class of
phosphorus-containing organic compound with a stable
direct C-P bond rather than a C-O-P linkage. A number of
bacterial species have operons, typically about 14 genes
in size, with genes for ATP-dependent transport of
phosphonates, degradation, and regulation of the
expression of the system. Members of this protein family
are the ATP-binding cassette component of tripartite ABC
transporters of phosphonates [Transport and binding
proteins, Anions].
Length = 243
Score = 28.8 bits (65), Expect = 4.1
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 12/64 (18%)
Query: 136 FNAIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGKSNVIDSMLFVFGYRASKIRANKLSVL 195
F AIIGP+G+GKS ++ + N ++ P+ + G +K+R KL L
Sbjct: 30 FVAIIGPSGAGKSTLLRCI----NRLVEPSSGSI--------LLEGTDITKLRGKKLRKL 77
Query: 196 MHKS 199
+
Sbjct: 78 RRRI 81
>gnl|CDD|213215 cd03248, ABCC_TAP, ATP-binding cassette domain of the Transporter
Associated with Antigen Processing, subfamily C. TAP
(Transporter Associated with Antigen Processing) is
essential for peptide delivery from the cytosol into the
lumen of the endoplasmic reticulum (ER), where these
peptides are loaded on major histocompatibility complex
(MHC) I molecules. Loaded MHC I leave the ER and display
their antigenic cargo on the cell surface to cytotoxic T
cells. Subsequently, virus-infected or malignantly
transformed cells can be eliminated. TAP belongs to the
large family of ATP-binding cassette (ABC) transporters,
which translocate a vast variety of solutes across
membranes.
Length = 226
Score = 29.0 bits (65), Expect = 4.2
Identities = 11/21 (52%), Positives = 17/21 (80%), Gaps = 1/21 (4%)
Query: 138 AIIGPNGSGKSNVIDSMLFRF 158
A++GP+GSGKS V+ ++L F
Sbjct: 44 ALVGPSGSGKSTVV-ALLENF 63
>gnl|CDD|224042 COG1117, PstB, ABC-type phosphate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 253
Score = 29.0 bits (66), Expect = 4.2
Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 138 AIIGPNGSGKSNVIDSMLFRFNAII 162
A+IGP+G GKS ++ L R N +I
Sbjct: 37 ALIGPSGCGKSTLL-RCLNRMNDLI 60
>gnl|CDD|213209 cd03242, ABC_RecF, ATP-binding cassette domain of RecF. RecF is a
recombinational DNA repair ATPase that maintains
replication in the presence of DNA damage. When
replication is prematurely disrupted by DNA damage,
several recF pathway gene products play critical roles
processing the arrested replication fork, allowing it to
resume and complete its task. This CD represents the
nucleotide binding domain of RecF. RecF belongs to a
large superfamily of ABC transporters involved in the
transport of a wide variety of different compounds
including sugars, ions, peptides, and more complex
organic molecules. The nucleotide binding domain shows
the highest similarity between all members of the
family. ABC transporters are a subset of nucleotide
hydrolases with a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 270
Score = 28.8 bits (65), Expect = 4.2
Identities = 5/23 (21%), Positives = 13/23 (56%)
Query: 134 KRFNAIIGPNGSGKSNVIDSMLF 156
++G N GK+N+++++
Sbjct: 21 PGVTVLVGENAQGKTNLLEAISL 43
Score = 28.8 bits (65), Expect = 5.0
Identities = 5/20 (25%), Positives = 13/20 (65%)
Query: 159 NAIIGPNGSGKSNVIDSMLF 178
++G N GK+N+++++
Sbjct: 24 TVLVGENAQGKTNLLEAISL 43
>gnl|CDD|236861 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed.
Length = 635
Score = 29.1 bits (66), Expect = 4.5
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 138 AIIGPNGSGKSNVIDSML 155
A+IGPNG GK+ ++ ML
Sbjct: 349 ALIGPNGCGKTTLLKLML 366
Score = 29.1 bits (66), Expect = 4.5
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 160 AIIGPNGSGKSNVIDSML 177
A+IGPNG GK+ ++ ML
Sbjct: 349 ALIGPNGCGKTTLLKLML 366
>gnl|CDD|216796 pfam01935, DUF87, Domain of unknown function DUF87. The function
of this prokaryotic domain is unknown. It contains
several conserved aspartates and histidines that could
be metal ligands.
Length = 218
Score = 28.5 bits (64), Expect = 4.9
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 151 IDSMLFRFNAIIGPNGSGKSN 171
++ ++ R AI+G GSGKSN
Sbjct: 18 LNKLVSRHFAILGSTGSGKSN 38
>gnl|CDD|233193 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 29.2 bits (66), Expect = 4.9
Identities = 8/27 (29%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 138 AIIGPNGSGKS---NVIDSMLFRFNAI 161
I GP GSGK+ N + + + ++ +
Sbjct: 438 LIFGPTGSGKTTLLNFLLAQMQKYGGM 464
>gnl|CDD|188099 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 [Transport and
binding proteins, Anions].
Length = 247
Score = 28.8 bits (65), Expect = 4.9
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 138 AIIGPNGSGKSNVIDSM 154
A+IGP+G GKS ++ S+
Sbjct: 31 ALIGPSGCGKSTLLRSL 47
Score = 28.8 bits (65), Expect = 4.9
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 160 AIIGPNGSGKSNVIDSM 176
A+IGP+G GKS ++ S+
Sbjct: 31 ALIGPSGCGKSTLLRSL 47
>gnl|CDD|214372 CHL00131, ycf16, sulfate ABC transporter protein; Validated.
Length = 252
Score = 28.5 bits (64), Expect = 5.1
Identities = 10/11 (90%), Positives = 11/11 (100%)
Query: 138 AIIGPNGSGKS 148
AI+GPNGSGKS
Sbjct: 37 AIMGPNGSGKS 47
Score = 28.5 bits (64), Expect = 5.1
Identities = 10/11 (90%), Positives = 11/11 (100%)
Query: 160 AIIGPNGSGKS 170
AI+GPNGSGKS
Sbjct: 37 AIMGPNGSGKS 47
>gnl|CDD|172744 PRK14256, PRK14256, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 252
Score = 28.4 bits (63), Expect = 5.1
Identities = 16/45 (35%), Positives = 24/45 (53%)
Query: 132 RYKRFNAIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGKSNVIDSM 176
+ ++ N G N + K +D AIIGP+G GKS V+ S+
Sbjct: 6 KLEQLNVHFGKNHAVKDVSMDFPENSVTAIIGPSGCGKSTVLRSI 50
>gnl|CDD|147120 pfam04803, Cor1, Cor1/Xlr/Xmr conserved region. Cor1 is a
component of the chromosome core in the meiotic prophase
chromosomes. Xlr is a lymphoid cell specific protein.
Xlm is abundantly transcribed in testis in a
tissue-specific and developmentally regulated manner.
The protein is located in the nuclei of spermatocytes,
early in the prophase of the first meiotic division, and
later becomes concentrated in the XY nuclear subregion
where it is in particular associated with the axes of
sex chromosomes.
Length = 130
Score = 27.7 bits (62), Expect = 5.2
Identities = 25/111 (22%), Positives = 48/111 (43%), Gaps = 20/111 (18%)
Query: 284 KMEVLYGKYDEERTEK--------LTRVQLVETDLKALEPELRKAVNFLELENCVQRKHN 335
K+E ++ E+R + LT Q E D + E + K N R+
Sbjct: 25 KLEQVWKTQQEQRQKLNQEYSQQFLTLFQQWEADAQKFEEQEEKLSNMF-------RQQQ 77
Query: 336 EIYQYERYVNMKNLGEHETKVQQMEQELTANLESIKKCTDEM-ESAKTELK 385
+++Q R V + L ++++ ++ NLE ++K D + A+ EL+
Sbjct: 78 KLFQQARIVQNQRLKT----IKELHEQFLKNLEELEKSHDNFLQGAQEELR 124
>gnl|CDD|226969 COG4618, ArpD, ABC-type protease/lipase transport system, ATPase
and permease components [General function prediction
only].
Length = 580
Score = 28.8 bits (65), Expect = 5.2
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 138 AIIGPNGSGKS 148
IIGP+GSGKS
Sbjct: 366 GIIGPSGSGKS 376
Score = 28.8 bits (65), Expect = 5.2
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 160 AIIGPNGSGKS 170
IIGP+GSGKS
Sbjct: 366 GIIGPSGSGKS 376
>gnl|CDD|163431 TIGR03719, ABC_ABC_ChvD, ATP-binding cassette protein, ChvD family.
Members of this protein family have two copies of the
ABC transporter ATP-binding cassette, but are found
outside the common ABC transporter operon structure that
features integral membrane permease proteins and
substrate-binding proteins encoded next to the
ATP-binding cassette (ABC domain) protein. The member
protein ChvD from Agrobacterium tumefaciens was
identified as both a candidate to interact with VirB8,
based on yeast two-hybrid analysis, and as an apparent
regulator of VirG. The general function of this protein
family is unknown.
Length = 552
Score = 28.7 bits (65), Expect = 5.2
Identities = 25/93 (26%), Positives = 35/93 (37%), Gaps = 24/93 (25%)
Query: 101 EVEQISMMPPKGKTEKETGLLEYLEEIIGTNRYKR--FNAIIGPNGS------------- 145
E+E + PK + K L EE++ KR I P G
Sbjct: 271 ELEWVRS-SPKARQAKSKARLARYEELLSQEFQKRNETAEIYIPPGPRLGDKVIEAENLS 329
Query: 146 ---GKSNVIDSMLFRFNA-----IIGPNGSGKS 170
G +ID + F+ +IGPNG+GKS
Sbjct: 330 KGFGDKLLIDDLSFKLPPGGIVGVIGPNGAGKS 362
Score = 28.4 bits (64), Expect = 8.9
Identities = 29/103 (28%), Positives = 38/103 (36%), Gaps = 46/103 (44%)
Query: 56 EVYIPPIAPVCFADPTGPRLIITKIVAFNF-KSYAGYVTLGPFNTGEVEQISMMPPKGKT 114
E+YIPP GPRL I A N K + + ++ +S P G
Sbjct: 309 EIYIPP----------GPRLGDKVIEAENLSKGFGDKLL--------IDDLSFKLPPGG- 349
Query: 115 EKETGLLEYLEEIIGTNRYKRFNAIIGPNGSGKSNVIDSMLFR 157
I+G +IGPNG+GKS LFR
Sbjct: 350 ------------IVG---------VIGPNGAGKST-----LFR 366
>gnl|CDD|227019 COG4674, COG4674, Uncharacterized ABC-type transport system, ATPase
component [General function prediction only].
Length = 249
Score = 28.5 bits (64), Expect = 5.3
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 138 AIIGPNGSGKSNVID 152
+IGPNG+GK+ ++D
Sbjct: 35 VLIGPNGAGKTTLMD 49
Score = 28.5 bits (64), Expect = 5.3
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 160 AIIGPNGSGKSNVID 174
+IGPNG+GK+ ++D
Sbjct: 35 VLIGPNGAGKTTLMD 49
>gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein
MsbA. This family consists of a single polypeptide
chain transporter in the ATP-binding cassette (ABC)
transporter family, MsbA, which exports lipid A. It may
also act in multidrug resistance. Lipid A, a part of
lipopolysaccharide, is found in the outer leaflet of the
outer membrane of most Gram-negative bacteria. Members
of this family are restricted to the Proteobacteria
(although lipid A is more broadly distributed) and often
are clustered with lipid A biosynthesis genes [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides, Transport and
binding proteins, Other].
Length = 571
Score = 28.9 bits (65), Expect = 5.4
Identities = 9/21 (42%), Positives = 17/21 (80%), Gaps = 1/21 (4%)
Query: 138 AIIGPNGSGKSNVIDSMLFRF 158
A++G +GSGKS ++ +++ RF
Sbjct: 362 ALVGRSGSGKSTLV-NLIPRF 381
>gnl|CDD|213197 cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the
drug resistance transporter and related proteins,
subfamily A. This family of ATP-binding proteins
belongs to a multi-subunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid transport,
and lantibiotic immunity. In bacteria and archaea, these
transporters usually include an ATP-binding protein and
one or two integral membrane proteins. Eukaryotic
systems of the ABCA subfamily display ABC domains that
are quite similar to this family. The ATP-binding domain
shows the highest similarity between all members of the
ABC transporter family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 173
Score = 28.1 bits (64), Expect = 5.4
Identities = 6/11 (54%), Positives = 10/11 (90%)
Query: 138 AIIGPNGSGKS 148
++GPNG+GK+
Sbjct: 30 GLLGPNGAGKT 40
Score = 28.1 bits (64), Expect = 5.4
Identities = 6/11 (54%), Positives = 10/11 (90%)
Query: 160 AIIGPNGSGKS 170
++GPNG+GK+
Sbjct: 30 GLLGPNGAGKT 40
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 28.7 bits (65), Expect = 5.5
Identities = 15/41 (36%), Positives = 19/41 (46%), Gaps = 11/41 (26%)
Query: 131 NRYKRFNAIIGPNGS--GKSNVIDSMLFRFNAIIGPNGSGK 169
N YKR N + KSN++ +IGP GSGK
Sbjct: 79 NHYKRLNNKEDNDDVELSKSNIL---------LIGPTGSGK 110
>gnl|CDD|226637 COG4167, SapF, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 267
Score = 28.6 bits (64), Expect = 5.6
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 9/54 (16%)
Query: 138 AIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGKSNVIDSMLFVFG---YRASKIR 188
AIIG NGSGKS L + A + SG+ +I+ FG +R+ +IR
Sbjct: 43 AIIGENGSGKST-----LAKMLAGMIEPTSGEI-LINDHPLHFGDYSFRSKRIR 90
>gnl|CDD|234357 TIGR03797, NHLM_micro_ABC2, NHLM bacteriocin system ABC
transporter, ATP-binding protein. Members of this
protein family are ABC transporter ATP-binding subunits,
part of a three-gene putative bacteriocin transport
operon. The other subunits include another ATP-binding
subunit (TIGR03796), which has an N-terminal leader
sequence cleavage domain, and an HlyD homolog
(TIGR03794). In a number of genomes, members of protein
families related to nitrile hydratase alpha subunit or
to nif11 have undergone paralogous family expansions,
with members possessing a putative bacteriocin cleavage
region ending with a classic Gly-Gly motif. Those sets
of putative bacteriocins, members of this protein family
and its partners TIGR03794 and TIGR03796, and
cyclodehydratase/docking scaffold fusion proteins of
thiazole/oxazole biosynthesis frequently show correlated
species distribution and co-clustering within many of
those genomes [Transport and binding proteins, Amino
acids, peptides and amines, Cellular processes,
Biosynthesis of natural products].
Length = 686
Score = 28.8 bits (65), Expect = 5.6
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 5/22 (22%)
Query: 136 FNAIIGPNGSGKSNVIDSMLFR 157
F AI+GP+GSGKS L R
Sbjct: 481 FVAIVGPSGSGKST-----LLR 497
Score = 28.4 bits (64), Expect = 7.2
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 158 FNAIIGPNGSGKS 170
F AI+GP+GSGKS
Sbjct: 481 FVAIVGPSGSGKS 493
>gnl|CDD|226963 COG4604, CeuD, ABC-type enterochelin transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 252
Score = 28.4 bits (64), Expect = 5.7
Identities = 12/20 (60%), Positives = 17/20 (85%), Gaps = 1/20 (5%)
Query: 138 AIIGPNGSGKSNVIDSMLFR 157
+IIGPNG+GKS ++ SM+ R
Sbjct: 31 SIIGPNGAGKSTLL-SMMSR 49
>gnl|CDD|227590 COG5265, ATM1, ABC-type transport system involved in Fe-S cluster
assembly, permease and ATPase components
[Posttranslational modification, protein turnover,
chaperones].
Length = 497
Score = 28.9 bits (65), Expect = 5.7
Identities = 12/21 (57%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 138 AIIGPNGSGKSNVIDSMLFRF 158
AI+G +G+GKS I +LFRF
Sbjct: 293 AIVGESGAGKS-TILRLLFRF 312
>gnl|CDD|184210 PRK13651, PRK13651, cobalt transporter ATP-binding subunit;
Provisional.
Length = 305
Score = 28.5 bits (64), Expect = 5.7
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 4/30 (13%)
Query: 136 FNAIIGPNGSGKSNVIDSMLFRFNAIIGPN 165
F AIIG GSGK+ I+ + NA++ P+
Sbjct: 35 FIAIIGQTGSGKTTFIEHL----NALLLPD 60
>gnl|CDD|234189 TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB
family. Type I protein secretion is a system in some
Gram-negative bacteria to export proteins (often
proteases) across both inner and outer membranes to the
extracellular medium. This is one of three proteins of
the type I secretion apparatus. Targeted proteins are
not cleaved at the N-terminus, but rather carry signals
located toward the extreme C-terminus to direct type I
secretion. This model is related to models TIGR01842 and
TIGR01846, and to bacteriocin ABC transporters that
cleave their substrates during export [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 694
Score = 28.7 bits (65), Expect = 5.8
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 138 AIIGPNGSGKS 148
AIIG GSGKS
Sbjct: 495 AIIGRIGSGKS 505
Score = 28.7 bits (65), Expect = 5.8
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 160 AIIGPNGSGKS 170
AIIG GSGKS
Sbjct: 495 AIIGRIGSGKS 505
>gnl|CDD|226425 COG3910, COG3910, Predicted ATPase [General function prediction
only].
Length = 233
Score = 28.2 bits (63), Expect = 5.9
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 9/57 (15%)
Query: 139 IIGPNGSGKSNVIDSM--LFRFNAIIGP-NGSGKSNVIDSMLFVFGYRASKIRANKL 192
I G NGSGKS +++++ FNA G N G+ + S L + +K
Sbjct: 42 ITGENGSGKSTLLEAIAAGMGFNAAGGGKNFKGELDASHSAL------VDYAKLHKR 92
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 28.8 bits (65), Expect = 6.1
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 160 AIIGPNGSGKSNVIDSMLFVFGYRASKIR 188
AI+GPNG+GKS ++ + G + ++
Sbjct: 352 AIVGPNGAGKSTLLKLLAGELGPLSGTVK 380
Score = 28.8 bits (65), Expect = 6.6
Identities = 9/11 (81%), Positives = 11/11 (100%)
Query: 138 AIIGPNGSGKS 148
AI+GPNG+GKS
Sbjct: 352 AIVGPNGAGKS 362
>gnl|CDD|200948 pfam00038, Filament, Intermediate filament protein.
Length = 312
Score = 28.3 bits (64), Expect = 6.2
Identities = 32/127 (25%), Positives = 54/127 (42%), Gaps = 24/127 (18%)
Query: 278 LQEPIAKMEVLYGKYDEERTEKLTRVQ---LVETDLKALEPELRKAV------------- 321
LQE +A ++ + +EE E +++Q VE D A + +L KA+
Sbjct: 129 LQEELAFLKKNH---EEEVRELQSQIQGQVNVEMD-AARKLDLTKALAEIRAQYEELAEK 184
Query: 322 NFLELENCVQRKHNEIYQYERYVNMKNLGEHETKVQQME---QELTANLESIKKCTDEME 378
N E E + K E+ Q N L + ++ ++ Q L L+S+KK +E
Sbjct: 185 NRQEAEEWYKSKLEEL-QQAAARNGDALRSAKEEITELRRQIQSLEIELQSLKKQKASLE 243
Query: 379 SAKTELK 385
EL+
Sbjct: 244 RQLAELE 250
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 28.9 bits (64), Expect = 6.2
Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 5/32 (15%)
Query: 138 AIIGPNGSGKSNVIDSMLFRF-----NAIIGP 164
A++GP G+GKS +I S++ RF + I GP
Sbjct: 73 AVVGPPGTGKSTLIRSLVRRFTKQTIDEIRGP 104
>gnl|CDD|233665 TIGR01978, sufC, FeS assembly ATPase SufC. SufC is part of the SUF
system, shown in E. coli to consist of six proteins and
believed to act in Fe-S cluster formation during
oxidative stress. SufC forms a complex with SufB and
SufD. SufC belongs to the ATP-binding cassette
transporter family (pfam00005) but is no longer thought
to be part of a transporter. The complex is reported as
cytosolic (PMID:12554644) or associated with the
membrane (PMID:11943156). The SUF system also includes a
cysteine desulfurase (SufS, enhanced by SufE) and a
probable iron-sulfur cluster assembly scaffold protein,
SufA [Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 243
Score = 28.4 bits (64), Expect = 6.2
Identities = 10/11 (90%), Positives = 11/11 (100%)
Query: 138 AIIGPNGSGKS 148
AI+GPNGSGKS
Sbjct: 30 AIMGPNGSGKS 40
Score = 28.4 bits (64), Expect = 6.2
Identities = 10/11 (90%), Positives = 11/11 (100%)
Query: 160 AIIGPNGSGKS 170
AI+GPNGSGKS
Sbjct: 30 AIMGPNGSGKS 40
>gnl|CDD|218636 pfam05557, MAD, Mitotic checkpoint protein. This family consists
of several eukaryotic mitotic checkpoint (Mitotic arrest
deficient or MAD) proteins. The mitotic spindle
checkpoint monitors proper attachment of the bipolar
spindle to the kinetochores of aligned sister chromatids
and causes a cell cycle arrest in prometaphase when
failures occur. Multiple components of the mitotic
spindle checkpoint have been identified in yeast and
higher eukaryotes. In S.cerevisiae, the existence of a
Mad1-dependent complex containing Mad2, Mad3, Bub3 and
Cdc20 has been demonstrated.
Length = 722
Score = 28.7 bits (64), Expect = 6.4
Identities = 22/104 (21%), Positives = 40/104 (38%), Gaps = 6/104 (5%)
Query: 281 PIAKMEVLYGKYDEERTEKL-TRVQL--VETDLKALEPELRKAVNFLELENCVQRKHNEI 337
+ +V +R E + ++ +L +E +L E E ++A LE + ++ E
Sbjct: 45 SSLQKQVEESMTLLQRAELIRSKSKLIQLENELMQKELEHKRAQIELERKASTLAENYER 104
Query: 338 ---YQYERYVNMKNLGEHETKVQQMEQELTANLESIKKCTDEME 378
E V +K L E E K + E + +K D
Sbjct: 105 ELDRNLELEVRLKALEELEKKAENEAAEAEEEAKLLKDKLDAES 148
>gnl|CDD|213191 cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of
branched-chain amino acid transporter. LivF (TM1139) is
part of the LIV-I bacterial ABC-type two-component
transport system that imports neutral, branched-chain
amino acids. The E. coli branched-chain amino acid
transporter comprises a heterodimer of ABC transporters
(LivF and LivG), a heterodimer of six-helix TM domains
(LivM and LivH), and one of two alternative soluble
periplasmic substrate binding proteins (LivK or LivJ).
ABC transporters are a large family of proteins involved
in the transport of a wide variety of different
compounds, like sugars, ions, peptides, and more complex
organic molecules.
Length = 222
Score = 28.2 bits (64), Expect = 6.4
Identities = 8/26 (30%), Positives = 15/26 (57%), Gaps = 7/26 (26%)
Query: 138 AIIGPNGSGKSNVIDSMLFRFNAIIG 163
A++G NG+GK+ ++ I+G
Sbjct: 30 ALLGRNGAGKTTLL-------KTIMG 48
Score = 27.8 bits (63), Expect = 8.6
Identities = 6/11 (54%), Positives = 10/11 (90%)
Query: 160 AIIGPNGSGKS 170
A++G NG+GK+
Sbjct: 30 ALLGRNGAGKT 40
>gnl|CDD|172750 PRK14262, PRK14262, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 250
Score = 28.3 bits (63), Expect = 6.5
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 125 EEIIGTNRYKRFNAIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGKSNVIDSM 176
E II + F+A G + K+ + + AIIGP+G GK+ ++ S+
Sbjct: 1 EPII---EIENFSAYYGEKKAVKNVTMKIFKNQITAIIGPSGCGKTTLLRSI 49
>gnl|CDD|184584 PRK14238, PRK14238, phosphate transporter ATP-binding protein;
Provisional.
Length = 271
Score = 28.3 bits (63), Expect = 6.5
Identities = 17/53 (32%), Positives = 25/53 (47%)
Query: 138 AIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGKSNVIDSMLFVFGYRASKIRAN 190
AIIGP+G GKS I ++ + +GK D +F Y ++R N
Sbjct: 54 AIIGPSGCGKSTYIKTLNRMVELVPSVKTTGKILYRDQNIFDKSYSVEELRTN 106
>gnl|CDD|224051 COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase
component [Amino acid transport and metabolism].
Length = 240
Score = 28.2 bits (64), Expect = 6.8
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 138 AIIGPNGSGKS 148
IIGP+GSGKS
Sbjct: 32 VIIGPSGSGKS 42
Score = 28.2 bits (64), Expect = 6.8
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 160 AIIGPNGSGKS 170
IIGP+GSGKS
Sbjct: 32 VIIGPSGSGKS 42
>gnl|CDD|236992 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
Reviewed.
Length = 556
Score = 28.5 bits (65), Expect = 7.1
Identities = 11/19 (57%), Positives = 13/19 (68%), Gaps = 5/19 (26%)
Query: 139 IIGPNGSGKSNVIDSMLFR 157
IIGPNG+GKS LF+
Sbjct: 355 IIGPNGAGKST-----LFK 368
>gnl|CDD|184261 PRK13705, PRK13705, plasmid-partitioning protein SopA; Provisional.
Length = 388
Score = 28.4 bits (63), Expect = 7.1
Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 7/63 (11%)
Query: 173 IDSMLFVFGYRASKIRANK---LSVLMHKSDQVGGVSRCSVAIHFAQIIDKPNEEYEIIP 229
I+ M VFG R + + V HK GGV + SV++H AQ + ++
Sbjct: 87 INHMRDVFGTRLRRAEDVFPPVIGVAAHK----GGVYKTSVSVHLAQDLALKGLRVLLVE 142
Query: 230 GTD 232
G D
Sbjct: 143 GND 145
>gnl|CDD|163483 TIGR03771, anch_rpt_ABC, anchored repeat-type ABC transporter,
ATP-binding subunit. This protein family is the
ATP-binding cassette subunit of binding
protein-dependent ABC transporter complex that strictly
co-occurs with TIGR03769. TIGRFAMs model TIGR03769
describes a protein domain that occurs singly or as one
of up to three repeats in proteins of a number of
Actinobacteria, including Propionibacterium acnes
KPA171202. The TIGR03769 domain occurs both in an
adjacent gene for the substrate-binding protein and in
additional (often nearby) proteins, often with
LPXTG-like sortase recognition signals. Homologous
ATP-binding subunits outside the scope of this family
include manganese transporter MntA in Synechocystis sp.
PCC 6803 and chelated iron transporter subunits. The
function of this transporter complex is unknown
[Transport and binding proteins, Unknown substrate].
Length = 223
Score = 27.9 bits (62), Expect = 7.2
Identities = 7/30 (23%), Positives = 18/30 (60%)
Query: 160 AIIGPNGSGKSNVIDSMLFVFGYRASKIRA 189
++GPNG+GK+ ++ ++L + ++
Sbjct: 10 GLLGPNGAGKTTLLRAILGLIPPAKGTVKV 39
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 28.3 bits (64), Expect = 7.3
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 138 AIIGPNGSGKS 148
AI+G +GSGKS
Sbjct: 503 AIVGRSGSGKS 513
Score = 28.3 bits (64), Expect = 7.3
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 160 AIIGPNGSGKS 170
AI+G +GSGKS
Sbjct: 503 AIVGRSGSGKS 513
>gnl|CDD|226164 COG3638, COG3638, ABC-type phosphate/phosphonate transport system,
ATPase component [Inorganic ion transport and
metabolism].
Length = 258
Score = 28.0 bits (63), Expect = 7.4
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 136 FNAIIGPNGSGKSNVIDSM 154
AIIGP+G+GKS ++ S+
Sbjct: 32 MVAIIGPSGAGKSTLLRSL 50
Score = 28.0 bits (63), Expect = 7.4
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 158 FNAIIGPNGSGKSNVIDSM 176
AIIGP+G+GKS ++ S+
Sbjct: 32 MVAIIGPSGAGKSTLLRSL 50
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 28.4 bits (64), Expect = 7.7
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 159 NAIIGPNGSGKSNVIDSMLFV-FGYRASKIRANKL 192
I G NG+GKS +++++ F FG I+ +L
Sbjct: 30 TLITGKNGAGKSTMLEALTFALFGKPFRDIKKGQL 64
>gnl|CDD|184205 PRK13646, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 286
Score = 28.2 bits (63), Expect = 7.8
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 135 RFNAIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGKSNVID 174
++ AI+G GSGKS +I NA++ P +G V D
Sbjct: 34 KYYAIVGQTGSGKSTLIQ----NINALLKPT-TGTVTVDD 68
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 28.5 bits (64), Expect = 7.9
Identities = 20/102 (19%), Positives = 48/102 (47%), Gaps = 7/102 (6%)
Query: 276 LILQEPIAKMEVLYGKYDEERTEKLTRVQLVETDLKALEPELRKAVNFLELENCVQRKHN 335
+L++ A +E L + E RTE+L + Q+VE +L +L A+ Q K
Sbjct: 696 QLLEQQQAFLEALKDDFRELRTERLAKWQVVEGELDNQLAQLSAAIEAAR----TQAKA- 750
Query: 336 EIYQYERYVN--MKNLGEHETKVQQMEQELTANLESIKKCTD 375
+ + ++ + + +L V+++++++ +I++
Sbjct: 751 RLKELKKQYDRELASLDVDPNTVKELKRQIEELETTIERIAV 792
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 28.0 bits (63), Expect = 8.0
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 5/30 (16%)
Query: 146 GKSNVIDSMLFRFN-----AIIGPNGSGKS 170
G +D + F ++GPNG+GK+
Sbjct: 16 GDKTALDGVSFEVEPGEIFGLLGPNGAGKT 45
Score = 28.0 bits (63), Expect = 8.8
Identities = 6/11 (54%), Positives = 10/11 (90%)
Query: 138 AIIGPNGSGKS 148
++GPNG+GK+
Sbjct: 35 GLLGPNGAGKT 45
>gnl|CDD|226459 COG3950, COG3950, Predicted ATP-binding protein involved in
virulence [General function prediction only].
Length = 440
Score = 28.4 bits (63), Expect = 8.3
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 161 IIGPNGSGKSNVIDSM---LFVFGYRASKIRANKL 192
I+GPNGSGK+ V+D++ L F +R L
Sbjct: 29 IVGPNGSGKTTVLDAIRNALNKFIDFFIYLRFKSL 63
>gnl|CDD|172748 PRK14260, PRK14260, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 259
Score = 28.1 bits (62), Expect = 8.5
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 134 KRFNAIIGPNGSGKSNVIDSMLFRFNAIIGP 164
+ AIIGP+G GKS I L R + + GP
Sbjct: 33 NKVTAIIGPSGCGKSTFI-KTLNRISELEGP 62
>gnl|CDD|213196 cd03229, ABC_Class3, ATP-binding cassette domain of the binding
protein-dependent transport systems. This class is
comprised of all BPD (Binding Protein Dependent) systems
that are largely represented in archaea and eubacteria
and are primarily involved in scavenging solutes from
the environment. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides, and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 178
Score = 27.5 bits (62), Expect = 8.5
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 138 AIIGPNGSGKSNVI 151
A++GP+GSGKS ++
Sbjct: 30 ALLGPSGSGKSTLL 43
Score = 27.5 bits (62), Expect = 8.5
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 160 AIIGPNGSGKSNVI 173
A++GP+GSGKS ++
Sbjct: 30 ALLGPSGSGKSTLL 43
>gnl|CDD|172747 PRK14259, PRK14259, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 269
Score = 27.8 bits (62), Expect = 8.6
Identities = 17/36 (47%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 138 AIIGPNGSGKSNVIDSMLFRFNAIIGPNGSGKSNVI 173
A+IGP+G GKS V+ S L R N +I S K V+
Sbjct: 43 ALIGPSGCGKSTVLRS-LNRMNDLI-EGCSLKGRVL 76
>gnl|CDD|178268 PLN02662, PLN02662, cinnamyl-alcohol dehydrogenase family protein.
Length = 322
Score = 28.1 bits (63), Expect = 8.7
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 221 PNEEYEIIPGTDLEIARTAFYDNSS---YYTLNGKKVHFKEVAKVLRDHGVDL 270
PN Y + D+ A ++ S Y L + VH+ EV K+L + L
Sbjct: 219 PNASYRWVDVRDVANAHIQAFEIPSASGRYCLVERVVHYSEVVKILHELYPTL 271
>gnl|CDD|220637 pfam10223, DUF2181, Uncharacterized conserved protein (DUF2181).
This is region of approximately 250 residues conserved
from worms to humans. Its function is unknown.
Length = 244
Score = 27.8 bits (62), Expect = 8.9
Identities = 26/99 (26%), Positives = 43/99 (43%), Gaps = 14/99 (14%)
Query: 92 VTLGPFNTGEVEQISMM--PPKGKTEKETGLLEYLEEIIGTNR-----YKRFNAIIGPNG 144
V LG NTG ++ +M PP + L E+LEE++ + + +K A + P+
Sbjct: 32 VLLGGLNTGNEREVPIMAHPPA--IYSDITLEEWLEEVLKSQKGIKLDFKSIEA-VEPSL 88
Query: 145 SGKSNVIDSMLFR--FNAII--GPNGSGKSNVIDSMLFV 179
N+ D + NA I GP + + +D F
Sbjct: 89 DLLRNIYDPLKRPVWINADILPGPVSNTITTPVDPSTFF 127
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 28.3 bits (64), Expect = 9.0
Identities = 13/37 (35%), Positives = 26/37 (70%), Gaps = 1/37 (2%)
Query: 160 AIIGPNGSGKSNVIDSMLFVFGYRAS-KIRANKLSVL 195
A++GP+G+GK+++++++L Y+ S KI +L L
Sbjct: 380 ALVGPSGAGKTSLLNALLGFLPYQGSLKINGIELREL 416
>gnl|CDD|213213 cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of
PrtD, subfamily C. This family represents the ABC
component of the protease secretion system PrtD, a
60-kDa integral membrane protein sharing 37% identity
with HlyB, the ABC component of the alpha-hemolysin
secretion pathway, in the C-terminal domain. They export
degradative enzymes by using a type I protein secretion
system and lack an N-terminal signal peptide, but
contain a C-terminal secretion signal. The Type I
secretion apparatus is made up of three components, an
ABC transporter, a membrane fusion protein (MFP), and an
outer membrane protein (OMP). For the HlyA transporter
complex, HlyB (ABC transporter) and HlyD (MFP) reside in
the inner membrane of E. coli. The OMP component is
TolC, which is thought to interact with the MFP to form
a continuous channel across the periplasm from the
cytoplasm to the exterior. HlyB belongs to the family of
ABC transporters, which are ubiquitous, ATP-dependent
transmembrane pumps or channels. The spectrum of
transport substrates ranges from inorganic ions,
nutrients such as amino acids, sugars, or peptides,
hydrophobic drugs, to large polypeptides, such as HlyA.
Length = 173
Score = 27.6 bits (62), Expect = 9.1
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 138 AIIGPNGSGKSNVIDSML 155
AIIGP+GSGKS + +L
Sbjct: 32 AIIGPSGSGKSTLARLIL 49
Score = 27.6 bits (62), Expect = 9.1
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 160 AIIGPNGSGKSNVIDSML 177
AIIGP+GSGKS + +L
Sbjct: 32 AIIGPSGSGKSTLARLIL 49
>gnl|CDD|233207 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP)
Family protein. [Transport and binding proteins,
Other].
Length = 617
Score = 28.1 bits (63), Expect = 9.7
Identities = 11/48 (22%), Positives = 26/48 (54%)
Query: 110 PKGKTEKETGLLEYLEEIIGTNRYKRFNAIIGPNGSGKSNVIDSMLFR 157
+G +E L+ + G + A++G +G+GK+ +++++ FR
Sbjct: 27 LRGCFCRERPRKHLLKNVSGVAKPGELLAVMGSSGAGKTTLMNALAFR 74
>gnl|CDD|213229 cd03262, ABC_HisP_GlnQ, ATP-binding cassette domain of the
histidine and glutamine transporters. HisP and GlnQ are
the ATP-binding components of the bacterial periplasmic
histidine and glutamine permeases, respectively.
Histidine permease is a multi-subunit complex containing
the HisQ and HisM integral membrane subunits and two
copies of HisP. HisP has properties intermediate between
those of integral and peripheral membrane proteins and
is accessible from both sides of the membrane,
presumably by its interaction with HisQ and HisM. The
two HisP subunits form a homodimer within the complex.
The domain structure of the amino acid uptake systems is
typical for prokaryotic extracellular solute binding
protein-dependent uptake systems. All of the amino acid
uptake systems also have at least one, and in a few
cases, two extracellular solute binding proteins located
in the periplasm of Gram-negative bacteria, or attached
to the cell membrane of Gram-positive bacteria. The
best-studied member of the PAAT (polar amino acid
transport) family is the HisJQMP system of S.
typhimurium, where HisJ is the extracellular solute
binding proteins and HisP is the ABC protein.
Length = 213
Score = 27.5 bits (62), Expect = 10.0
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 138 AIIGPNGSGKSNVI 151
IIGP+GSGKS ++
Sbjct: 30 VIIGPSGSGKSTLL 43
Score = 27.5 bits (62), Expect = 10.0
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 160 AIIGPNGSGKSNVI 173
IIGP+GSGKS ++
Sbjct: 30 VIIGPSGSGKSTLL 43
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.315 0.135 0.380
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,691,877
Number of extensions: 1962848
Number of successful extensions: 2797
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2750
Number of HSP's successfully gapped: 328
Length of query: 388
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 289
Effective length of database: 6,546,556
Effective search space: 1891954684
Effective search space used: 1891954684
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: 42 (22.0 bits)
S2: 60 (27.3 bits)