RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780810|ref|YP_003065223.1| transcription termination
factor Rho [Candidatus Liberibacter asiaticus str. psy62]
(423 letters)
>gnl|CDD|31352 COG1158, Rho, Transcription termination factor [Transcription].
Length = 422
Score = 683 bits (1763), Expect = 0.0
Identities = 294/423 (69%), Positives = 357/423 (84%), Gaps = 1/423 (0%)
Query: 1 MSEMKLQELKNKSPTKLLAFAESLEIENANVMRKQELMFSILKVLSGRDVEIIGEGVIEV 60
++EM L ELKNK ++LL AE L IEN + +RKQ+L+F+ILK + + EI G+GV+E+
Sbjct: 1 VAEMSLTELKNKPLSELLELAEELGIENYSRLRKQDLIFAILKAQAEQGEEIFGDGVLEI 60
Query: 61 LQDGFGFLRSPDANYLAGPDDIYVSPSQIKSFSLKTGDTVEGSIRAPREGERYFALLKVN 120
L DGFGFLRS D++YL GPDDIYVSPSQI+ F+L+TGDTVEG +R P+EGERYFALLKV
Sbjct: 61 LPDGFGFLRSADSSYLPGPDDIYVSPSQIRRFNLRTGDTVEGKVRPPKEGERYFALLKVE 120
Query: 121 AINFDVPERVRNKIHFDNLTPLYPDKRFNMELNNPENKDISSRVIDLIAPIGKGQRSLIV 180
A+N D PE+ +N++ F+NLTPLYP++R +E + D+S+RVIDLI+PIGKGQR LIV
Sbjct: 121 AVNGDDPEKAKNRVLFENLTPLYPNERLKLERE-NGSTDLSTRVIDLISPIGKGQRGLIV 179
Query: 181 APPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRSVQGEVISSTFDESAA 240
APP+ GKT LLQNIA++I NHPEC LIVLLIDERPEEVTDMQRSV+GEV++STFDE +
Sbjct: 180 APPKAGKTTLLQNIANAITTNHPECELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPPS 239
Query: 241 RHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNVLMPSSGKILTGGVDANALQRP 300
RHVQVAEMVI KAK LVE+G DVVILLDSITRL RAYN ++PSSGK+L+GGVDANAL RP
Sbjct: 240 RHVQVAEMVIEKAKRLVEHGKDVVILLDSITRLARAYNTVVPSSGKVLSGGVDANALHRP 299
Query: 301 KRFFGAARNIKEGGSLTIIGTALVDTGSRMDEVIFEEFKGTGNSEIVLERKIADKRIFPA 360
KRFFGAARNI+EGGSLTII TALVDTGSRMDEVIFEEFKGTGN E+ L+RK+A++RIFPA
Sbjct: 300 KRFFGAARNIEEGGSLTIIATALVDTGSRMDEVIFEEFKGTGNMELHLDRKLAERRIFPA 359
Query: 361 MDIIKSGTRKEDLLVERQDLQKVFMLRRIVSSMNSSDAIEFLIDKLKQTKDNKDFFYSMN 420
+DI KSGTRKE+LL+ +LQK+++LRRI+S M+ DAIEFLIDKLK+TK N +F MN
Sbjct: 360 IDINKSGTRKEELLLSPDELQKMWVLRRILSPMDEIDAIEFLIDKLKKTKTNDEFLEQMN 419
Query: 421 KQN 423
K
Sbjct: 420 KSK 422
>gnl|CDD|29994 cd01128, rho_factor, Transcription termination factor rho is a
bacterial ATP-dependent RNA/DNA helicase. It is a
homohexamer. Each monomer consists of an N-terminal
domain of the OB fold, which is responsible for binding
to cysteine rich nucleotides. This alignment is of the
C-terminal ATP binding domain..
Length = 249
Score = 421 bits (1083), Expect = e-118
Identities = 184/249 (73%), Positives = 226/249 (90%)
Query: 159 DISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEE 218
++S+RV+DL APIGKGQR LIVAPP+ GKT LLQ+IA++I KNHPE YLIVLLIDERPEE
Sbjct: 1 ELSTRVVDLFAPIGKGQRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEE 60
Query: 219 VTDMQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYN 278
VTDMQRSV+GEVI+STFDE RHVQVAEMV+ KAK LVE+G DVVILLDSITRL RAYN
Sbjct: 61 VTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEKAKRLVEHGKDVVILLDSITRLARAYN 120
Query: 279 VLMPSSGKILTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRMDEVIFEEF 338
++P SGKIL+GGVDANAL +PKRFFGAARNI+EGGSLTII TALVDTGSRMD+VIFEEF
Sbjct: 121 TVVPPSGKILSGGVDANALHKPKRFFGAARNIEEGGSLTIIATALVDTGSRMDDVIFEEF 180
Query: 339 KGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRIVSSMNSSDA 398
KGTGN E+VL+R++A++RIFPA+DI+KSGTRKE+LL++ ++LQ++++LRR++S M+ +A
Sbjct: 181 KGTGNMELVLDRRLAERRIFPAIDILKSGTRKEELLLDPEELQRMWLLRRVLSDMDPIEA 240
Query: 399 IEFLIDKLK 407
+EFL+ KL+
Sbjct: 241 MEFLLKKLR 249
>gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 234 bits (599), Expect = 4e-62
Identities = 71/214 (33%), Positives = 108/214 (50%), Gaps = 12/214 (5%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDM 222
R IDL+ PIGKGQR I TGKT+LL IA + K + E + +LI ER EV +
Sbjct: 4 RAIDLLLPIGKGQRIGIFGGSGTGKTVLLGMIARNAKADVVE---VYVLIGERGREVAEF 60
Query: 223 QRSVQGE-------VISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCR 275
+ GE V+++T DE A + A+ + G DV++LLDS+TR R
Sbjct: 61 IEELLGEGALKRTVVVAATSDEPPAERYLAPYTALTIAEYFRDQGKDVLLLLDSLTRFAR 120
Query: 276 AYNVLMPSSGKI-LTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRMDEVI 334
A + G+ G + R A ++ GGS+T + T LV G + + I
Sbjct: 121 ALREISLLLGEPPGREGYPGSLFSDLARLLERAGKVEGGGSITALPTVLVPGGD-ITDPI 179
Query: 335 FEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGT 368
+ + +IVL R++A++ I+PA+DI+ S +
Sbjct: 180 PDNTISITDGQIVLSRELAERGIYPAIDILLSVS 213
>gnl|CDD|88425 cd04459, Rho_CSD, Rho_CSD: Rho protein cold-shock domain (CSD). Rho
protein is a transcription termination factor in most
bacteria. In bacteria, there are two distinct mechanisms
for mRNA transcription termination. In intrinsic
termination, RNA polymerase and nascent mRNA are
released from DNA template by an mRNA stem loop
structure, which resembles the transcription termination
mechanism used by eukaryotic pol III. The second
mechanism is mediated by Rho factor. Rho factor
terminates transcription by using energy from ATP
hydrolysis to forcibly dissociate the transcripts from
RNA polymerase. Rho protein contains an N-terminal
S1-like domain, which binds single-stranded RNA. Rho has
a C-terminal ATPase domain which hydrolyzes ATP to
provide energy to strip RNA polymerase and mRNA from the
DNA template. Rho functions as a homohexamer..
Length = 68
Score = 119 bits (299), Expect = 2e-27
Identities = 51/68 (75%), Positives = 57/68 (83%)
Query: 54 GEGVIEVLQDGFGFLRSPDANYLAGPDDIYVSPSQIKSFSLKTGDTVEGSIRAPREGERY 113
G GV+E+L DGFGFLRS NYL GPDDIYVSPSQI+ F+L+TGDTV G IR P+EGERY
Sbjct: 1 GSGVLEILPDGFGFLRSSGYNYLPGPDDIYVSPSQIRRFNLRTGDTVVGQIRPPKEGERY 60
Query: 114 FALLKVNA 121
FALLKV A
Sbjct: 61 FALLKVEA 68
>gnl|CDD|31351 COG1157, FliI, Flagellar biosynthesis/type III secretory pathway
ATPase [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 441
Score = 108 bits (272), Expect = 2e-24
Identities = 75/254 (29%), Positives = 120/254 (47%), Gaps = 25/254 (9%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVL-LIDERPEEVTD 221
R ID + GKGQR I A GK+ LL IA + E + V+ LI ER EV +
Sbjct: 152 RAIDGLLTCGKGQRIGIFAGSGVGKSTLLGMIA-----RNTEADVNVIALIGERGREVRE 206
Query: 222 ----------MQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSIT 271
++RSV V+ +T DESA ++ A A+ + G V++++DS+T
Sbjct: 207 FIEKDLGEEGLKRSV---VVVATSDESALMRLKAAFTATTIAEYFRDQGKRVLLIMDSLT 263
Query: 272 RLCRAYNVLMPSSGKIL-TGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRM 330
R A + ++G+ T G + R A N + GS+T T LV+ G M
Sbjct: 264 RFAMAQREIGLAAGEPPATKGYPPSVFSELPRLLERAGN-GDKGSITAFYTVLVE-GDDM 321
Query: 331 DEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRIV 390
++ I +E + + IVL R +A+ +PA+D++ S +R +V + + LR+++
Sbjct: 322 NDPIADEVRSILDGHIVLSRALAEAGHYPAIDVLASISRVMPQIVSEEHRKAARRLRQLL 381
Query: 391 SSMNSSDAIEFLID 404
S E LI
Sbjct: 382 SRYE---ENEDLIR 392
>gnl|CDD|30002 cd01136, ATPase_flagellum-secretory_path_III, Flagellum-specific
ATPase/type III secretory pathway virulence-related
protein. This group of ATPases are responsible for the
export of flagellum and virulence-related proteins. The
bacterial flagellar motor is similar to the F0F1-ATPase,
in that they both are proton driven rotary molecular
devices. However, the main function of the bacterial
flagellar motor is to rotate the flagellar filament for
cell motility. Intracellular pathogens such as
Salmonella and Chlamydia also have proteins which are
similar to the flagellar-specific ATPase, but function
in the secretion of virulence-related proteins via the
type III secretory pathway..
Length = 326
Score = 106 bits (267), Expect = 8e-24
Identities = 80/281 (28%), Positives = 126/281 (44%), Gaps = 31/281 (11%)
Query: 137 DNLTPLYPDKRFNMELNNP---------ENKDISSRVIDLIAPIGKGQRSLIVAPPRTGK 187
D PL + R+ + P E R ID + +GKGQR I A GK
Sbjct: 23 DGKGPLGKEVRYPLLRTPPNPLKRRPIDEVLPTGVRAIDGLLTVGKGQRLGIFAGSGVGK 82
Query: 188 TILLQNIAHSIKKNHPECYLIVL-LIDERPEEVTD----------MQRSVQGEVISSTFD 236
+ LL IA + V+ LI ER EV + ++RSV V+ +T D
Sbjct: 83 STLLGMIA-----RGTTADVNVIALIGERGREVREFIEKDLGEEGLKRSV---VVVATSD 134
Query: 237 ESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNVLMPSSGKIL-TGGVDAN 295
ES V+ A A A+ + G DV++L+DS+TR A + ++G+ T G +
Sbjct: 135 ESPLLRVKAAYTATAIAEYFRDQGKDVLLLMDSLTRFAMAQREIGLAAGEPPTTKGYPPS 194
Query: 296 ALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRMDEVIFEEFKGTGNSEIVLERKIADK 355
R A N + GS+T T LV+ G ++E I + + + IVL R +A
Sbjct: 195 VFALLPRLLERAGN-SDKGSITAFYTVLVE-GDDLNEPIADAVRSILDGHIVLSRALAAA 252
Query: 356 RIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRIVSSMNSS 396
+PA+D++KS +R + +V + + LR ++S+
Sbjct: 253 GHYPAIDVLKSISRLMNAVVTPEHKEAARKLRELLSAYQEV 293
>gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion..
Length = 165
Score = 70.5 bits (172), Expect = 9e-13
Identities = 43/177 (24%), Positives = 74/177 (41%), Gaps = 18/177 (10%)
Query: 178 LIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTD-MQRSVQGEVISSTFD 236
L+ P +GKT L +A +I ++ + I+E EE+T+ + + +
Sbjct: 3 LVFGPTGSGKTTLALQLALNIAT--KGGKVVYVDIEEEIEELTERLIGESLKGALDNLII 60
Query: 237 ESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNVLMPSSGKILTGGVDANA 296
A A +++KA+ L E G D +I+LD +TRL RA + G
Sbjct: 61 VFATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALRE--------IREGYPGEL 112
Query: 297 LQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRMDEV---IFEEFKGTGNSEIVLER 350
+ + AR G +T+I T V +G + D + + ++ IVL R
Sbjct: 113 DEELRELLERARK----GGVTVIFTLQVPSGDKGDPRLTRGAQNLEDIADTVIVLSR 165
>gnl|CDD|29999 cd01133, F1-ATPase_beta, F1 ATP synthase beta subunit,
nucleotide-binding domain. The F-ATPase is found in
bacterial plasma membranes, mitochondrial inner
membranes and in chloroplast thylakoid membranes. It has
also been found in the archaea Methanosarcina barkeri.
It uses a proton gradient to drive ATP synthesis and
hydrolyzes ATP to build the proton gradient. The
extrinisic membrane domain, F1, is composed of alpha,
beta, gamma, delta and epsilon subunits with a
stoichiometry of 3:3:1:1:1. The beta subunit of ATP
synthase is catalytic..
Length = 274
Score = 58.6 bits (142), Expect = 3e-09
Identities = 69/264 (26%), Positives = 110/264 (41%), Gaps = 47/264 (17%)
Query: 137 DNLTPLYPDKRFNMELNNPENKDISS---------RVIDLIAPIGKGQRSLIVAPPRTGK 187
D P+ K + + PE + S+ +VIDL+AP KG + + GK
Sbjct: 23 DERGPIKTKKTWPIHREAPEFVEQSTKTEILETGIKVIDLLAPYAKGGKIGLFGGAGVGK 82
Query: 188 TILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRSV-QGEVISST------FDESAA 240
T+L+ + ++I K H Y + + ER E D+ + + V+S T +E
Sbjct: 83 TVLIMELINNIAKAH-GGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPG 141
Query: 241 RHVQVAEMVIAKAKCLVEY-----GLDVVILLDSITRLCRAYNVL------MPSS-GKIL 288
+VA + A EY G DV++ +D+I R +A + + MPS+ G
Sbjct: 142 ARARVALTGLTMA----EYFRDEEGQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQP 197
Query: 289 TGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRMDE---VIFEEFKGTGNSE 345
T + ALQ +R + GS+T + V D F T
Sbjct: 198 TLATEMGALQ--ERITSTKK-----GSITSVQAVYVPADDLTDPAPATTFAHLDAT---- 246
Query: 346 IVLERKIADKRIFPAMDIIKSGTR 369
VL R IA+ I+PA+D + S +R
Sbjct: 247 TVLSRAIAELGIYPAVDPLDSTSR 270
>gnl|CDD|30404 COG0055, AtpD, F0F1-type ATP synthase, beta subunit [Energy
production and conversion].
Length = 468
Score = 52.1 bits (125), Expect = 3e-07
Identities = 61/225 (27%), Positives = 98/225 (43%), Gaps = 30/225 (13%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDM 222
+VIDL+AP KG + + GKT+L+Q + ++I K H Y + + ER E D+
Sbjct: 136 KVIDLLAPYAKGGKIGLFGGAGVGKTVLIQELINNIAKEH-GGYSVFAGVGERTREGNDL 194
Query: 223 QRS-VQGEVISST------FDESAARHVQVAEMVIAKAKCLV-EYGLDVVILLDSITRLC 274
+ V+ T +E ++VA + A+ E G DV++ +D+I R
Sbjct: 195 YHEMKESGVLDKTALVFGQMNEPPGARMRVALTGLTMAEYFRDEEGQDVLLFIDNIFRFT 254
Query: 275 RAYNVL------MPSS-GKILTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTG 327
+A + + MPS+ G T + LQ +R + GS+T + V
Sbjct: 255 QAGSEVSALLGRMPSAVGYQPTLATEMGQLQ--ERITSTKK-----GSITSVQAVYVPAD 307
Query: 328 SRMDE---VIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTR 369
D F T VL R+IA I+PA+D + S +R
Sbjct: 308 DLTDPAPATTFAHLDAT----TVLSRQIAALGIYPAVDPLDSTSR 348
>gnl|CDD|36564 KOG1350, KOG1350, KOG1350, F0F1-type ATP synthase, beta subunit
[Energy production and conversion].
Length = 521
Score = 50.8 bits (121), Expect = 7e-07
Identities = 66/264 (25%), Positives = 115/264 (43%), Gaps = 31/264 (11%)
Query: 131 RNKIHFDNLTPLYPDKRFNMELN-NPENKDISSRVIDLIAPIGKGQRSLIVAPPRTGKTI 189
R I +P++ + +E++ E +V+DL+AP KG + + GKT+
Sbjct: 147 RGPIKSKKYSPIHAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTV 206
Query: 190 LLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRS-VQGEVISSTFDESAARHV--QVA 246
L+ + ++I K H Y + + ER E D+ ++ VI+ + S V Q+
Sbjct: 207 LIMELINNIAKAHGG-YSVFAGVGERTREGNDLYHEMIESGVINLEGETSKVALVYGQMN 265
Query: 247 EMVIAKAKC------LVEY-----GLDVVILLDSITRLCRAYNVL------MPSS-GKIL 288
E A+A+ + EY G DV++ +D+I R +A + + +PS+ G
Sbjct: 266 EPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQP 325
Query: 289 TGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRMDEVIFEEFKGTGNSEIVL 348
T D +Q +R + GS+T + V D F ++ VL
Sbjct: 326 TLATDMGTMQ--ERITTTKK-----GSITSVQAVYVPADDLTDPAPATTFAHL-DATTVL 377
Query: 349 ERKIADKRIFPAMDIIKSGTRKED 372
R IA+ I+PA+D + S +R D
Sbjct: 378 SRGIAELGIYPAVDPLDSTSRIMD 401
>gnl|CDD|30405 COG0056, AtpA, F0F1-type ATP synthase, alpha subunit [Energy
production and conversion].
Length = 504
Score = 42.9 bits (101), Expect = 2e-04
Identities = 32/122 (26%), Positives = 58/122 (47%), Gaps = 11/122 (9%)
Query: 164 VIDLIAPIGKGQRSLIVAPPRTGKT-ILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDM 222
ID + PIG+GQR LI+ +TGKT I + I + I + I ++ V ++
Sbjct: 152 AIDALIPIGRGQRELIIGDRQTGKTAIAIDTIINQKGSG---VKCIYVAIGQKRSTVANV 208
Query: 223 QRSVQGE-------VISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCR 275
R+++ V++++ +SA A A+ + G DV+I+ D +++
Sbjct: 209 VRTLEEHGAMDYTIVVAASASDSAPLQYLAPYAGCAMAEYFRDNGKDVLIVYDDLSKHAV 268
Query: 276 AY 277
AY
Sbjct: 269 AY 270
>gnl|CDD|29998 cd01132, F1_ATPase_alpha, F1 ATP synthase alpha, central domain.
The F-ATPase is found in bacterial plasma membranes,
mitochondrial inner membranes and in chloroplast
thylakoid membranes. It has also been found in the
archaea Methanosarcina barkeri. It uses a proton
gradient to drive ATP synthesis and hydrolyzes ATP to
build the proton gradient. The extrinisic membrane
domain, F1, is composed of alpha, beta, gamma, delta and
epsilon subunits with a stoichiometry of 3:3:1:1:1. The
alpha subunit of the F1 ATP synthase can bind
nucleotides, but is non-catalytic..
Length = 274
Score = 39.8 bits (93), Expect = 0.002
Identities = 30/123 (24%), Positives = 57/123 (46%), Gaps = 11/123 (8%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKT-ILLQNIAHSIKKNHPECYLIVLLIDERPEEVTD 221
+ ID + PIG+GQR LI+ +TGKT I + I + K Y I + I ++ V
Sbjct: 58 KAIDAMIPIGRGQRELIIGDRQTGKTAIAIDTIINQKGKK---VYCIYVAIGQKASTVAQ 114
Query: 222 MQRSVQGE-------VISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLC 274
+ ++++ V+++T + A A + ++ G +I+ D +++
Sbjct: 115 VVKTLEEHGAMEYTIVVAATASDPAPLQYLAPYTGCAMGEYFMDNGKHALIIYDDLSKQA 174
Query: 275 RAY 277
AY
Sbjct: 175 VAY 177
>gnl|CDD|30000 cd01134, V_A-ATPase_A, V/A-type ATP synthase catalytic subunit A.
These ATPases couple ATP hydrolysis to the build up of a
H+ gradient, but V-type ATPases do not catalyze the
reverse reaction. The Vacuolar (V-type) ATPase is found
in the membranes of vacuoles, the golgi apparatus and in
other coated vesicles in eukaryotes. Archaea have a
protein which is similar in sequence to V-ATPases, but
functions like an F-ATPase (called A-ATPase). A similar
protein is also found in a few bacteria..
Length = 369
Score = 39.4 bits (92), Expect = 0.002
Identities = 62/242 (25%), Positives = 100/242 (41%), Gaps = 60/242 (24%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTD- 221
RV+D + P+ KG + I P GKT++ S+ K +I + ER E+T+
Sbjct: 146 RVLDTLFPVVKGGTAAIPGPFGCGKTVI----QQSLSKYSNSDIVIYVGCGERGNEMTEV 201
Query: 222 ----------------MQRSVQGEVISSTFD-ESAARHVQVAEMVIAKAKCLVEY----G 260
M+R+V +I++T + AAR E I + EY G
Sbjct: 202 LEEFPELTDPVTGEPLMKRTV---LIANTSNMPVAAR-----EASIYTGITIAEYFRDMG 253
Query: 261 LDVVILLDSITRLCRAYNVLMPSSGKI----LTGGVDANALQRPKRFFGAARNIK----- 311
+V ++ DS +R A L SG++ G A R F+ A +K
Sbjct: 254 YNVALMADSTSRWAEA---LREISGRLEEMPGEEGYPAYLGARLASFYERAGRVKCLGSP 310
Query: 312 -EGGSLTIIGTALVDTGSRMDEV------IFEEFKGTGNSEIVLERKIADKRIFPAMDII 364
GS+TI+G G + V I + F G L++K+A +R FP+++ +
Sbjct: 311 GREGSVTIVGAVSPPGGDFSEPVTQATLRIVQVFWG-------LDKKLAQRRHFPSINWL 363
Query: 365 KS 366
S
Sbjct: 364 IS 365
>gnl|CDD|31349 COG1155, NtpA, Archaeal/vacuolar-type H+-ATPase subunit A [Energy
production and conversion].
Length = 588
Score = 38.7 bits (90), Expect = 0.003
Identities = 62/244 (25%), Positives = 104/244 (42%), Gaps = 48/244 (19%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTD- 221
RVID + P+ KG + + P +GKT+ H++ K +I + ER E+T+
Sbjct: 213 RVIDTLFPVAKGGTAAVPGPFGSGKTV----SQHTLSKLADGDIVIYVGCGERGNEMTEV 268
Query: 222 ----------------MQRSVQGEVISSTFD-ESAARHVQVAEMVIAKAKCLVEY----G 260
M R+V +I++T + AAR E I + EY G
Sbjct: 269 LQEFPELKDPNTGQPLMDRTV---LIANTSNMPVAAR-----EASIYTGITIAEYYRDMG 320
Query: 261 LDVVILLDSITRLCRAYNVLMPSSGKI--LTG--GVDANALQRPKRFF---GAARNI--- 310
DV ++ DS +R A L SG++ + G G A R F+ G R +
Sbjct: 321 YDVALMADSTSRWAEA---LREISGRLEEMPGEEGYPAYLGSRLAEFYERAGRVRLVSPE 377
Query: 311 KEGGSLTIIGTALVDTGSRMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRK 370
+ GS+T+IG A+ G E + + L+ +A++R FP+++ + S +
Sbjct: 378 ERFGSITVIG-AVSPPGGDFSEPVTQNTLRVVRVFWALDAALANRRHFPSINWLNSYSLY 436
Query: 371 EDLL 374
+ L
Sbjct: 437 TEDL 440
>gnl|CDD|176999 CHL00059, atpA, ATP synthase CF1 alpha subunit.
Length = 485
Score = 36.1 bits (84), Expect = 0.019
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 164 VIDLIAPIGKGQRSLIVAPPRTGKT 188
ID + PIG+GQR LI+ +TGKT
Sbjct: 131 AIDSMIPIGRGQRELIIGDRQTGKT 155
>gnl|CDD|30815 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 35.1 bits (80), Expect = 0.043
Identities = 32/150 (21%), Positives = 56/150 (37%), Gaps = 9/150 (6%)
Query: 173 KGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRSVQGEVIS 232
+G LI PP TGKTI + + + +E PEE+ + RS G +
Sbjct: 22 RGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYV--STEESPEELLENARSF-GWDLE 78
Query: 233 STFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCR---AYNVLMPSSGKILT 289
++ + +V LD+ LLD I + A V++ S ++
Sbjct: 79 VYIEKGKLAILDAFLSEKGLVSIVVGDPLDLEELLDRIREIVEKEGADRVVIDSITELTL 138
Query: 290 GGVDANALQRPKRFFGAARNIKEGGSLTII 319
++ AL R R + + +T +
Sbjct: 139 -YLNDPALVR--RILLLLKRFLKKLGVTSL 165
>gnl|CDD|72982 cd03223, ABCD_peroxisomal_ALDP, 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 = 33.2 bits (76), Expect = 0.14
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 149 NMELNNPENKDISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAH 196
N+ L P+ + + DL I G R LI P TGK+ L + +A
Sbjct: 5 NLSLATPDGR---VLLKDLSFEIKPGDRLLITGPSGTGKSSLFRALAG 49
>gnl|CDD|30003 cd01393, recA_like, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange. While prokaryotes have a single RecA
protein, eukaryotes have multiple RecA homologs such as
Rad51, DMC1 and Rad55/57. Archaea have the RecA-like
homologs radA and radB..
Length = 226
Score = 32.9 bits (75), Expect = 0.17
Identities = 23/117 (19%), Positives = 42/117 (35%), Gaps = 10/117 (8%)
Query: 179 IVAPPRTGKTILLQNIAHSIKKNHPECYL--IVLLID-------ERPEEVTDMQRSVQGE 229
I +GKT L +A + L V+ ID ER ++ E
Sbjct: 24 IFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERLVQLAVRFGLDPEE 83
Query: 230 VISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNVLMPSSGK 286
V+ + + Q E+V + + +D+V+ +DS+ L R + +
Sbjct: 84 VLDNIYVARPYNGEQQLEIVEELERIMSSGRVDLVV-VDSVAALFRKEFIGRGMLAE 139
>gnl|CDD|36285 KOG1067, KOG1067, KOG1067, Predicted RNA-binding polyribonucleotide
nucleotidyltransferase [General function prediction
only].
Length = 760
Score = 31.9 bits (72), Expect = 0.30
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 3/74 (4%)
Query: 154 NPENKDISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLID 213
NP K++SS ++L+ G +S V + IL Q++ H+IK E I+ I+
Sbjct: 205 NPTRKEMSSSQLNLVV---AGTKSQTVMLEGSSNNILQQDLLHAIKVGVKEAQQIIQGIE 261
Query: 214 ERPEEVTDMQRSVQ 227
++ +R Q
Sbjct: 262 RLAKKYGKQKREPQ 275
>gnl|CDD|33918 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 31.8 bits (72), Expect = 0.37
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 14/73 (19%)
Query: 124 FDVPERVRNKIHFDNLTPLYPDKRFNMELNNPENKDISSRVIDLIAPIGKGQRSLIVAPP 183
D + + I +NL+ L P+ + + + +L + G+R LI
Sbjct: 383 IDFDDNADHGITLENLS-----------LRTPDGQ---TLLSELNFEVRPGERLLITGES 428
Query: 184 RTGKTILLQNIAH 196
GKT LL+ +A
Sbjct: 429 GAGKTSLLRALAG 441
>gnl|CDD|35194 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 30.4 bits (68), Expect = 0.90
Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 2/72 (2%)
Query: 162 SRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNH--PECYLIVLLIDERPEEV 219
+ + + K + LI+ P +GKT LQ +A + + PE I LL++
Sbjct: 210 QDALPGLEALEKYAKLLILGAPGSGKTTFLQRLALWLAQRTLEPEDVPIFLLLNAFALAR 269
Query: 220 TDMQRSVQGEVI 231
++ + +
Sbjct: 270 KFEKQLSLIDYL 281
>gnl|CDD|36646 KOG1433, KOG1433, KOG1433, DNA repair protein RAD51/RHP55
[Replication, recombination and repair].
Length = 326
Score = 30.4 bits (68), Expect = 0.91
Identities = 18/88 (20%), Positives = 32/88 (36%), Gaps = 4/88 (4%)
Query: 171 IGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRSVQGEV 230
I G + +V PP +GKT L +A + + I R E +T + G
Sbjct: 108 IETGSLTELVGPPGSGKTQLCHTLAVTCGGGEGKVLYIDTESTFRLERLT----EIAGRS 163
Query: 231 ISSTFDESAARHVQVAEMVIAKAKCLVE 258
D + + A + + + + E
Sbjct: 164 GLRGRDTLSNLMLARAYNLDHQLQLIQE 191
>gnl|CDD|29989 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of
recombinases includes the eukaryotic proteins RAD51,
RAD55/57 and the meiosis-specific protein DMC1, and the
archaeal proteins radA and radB. They are closely
related to the bacterial RecA group. Rad51 proteins
catalyze a similiar recombination reaction as RecA,
using ATP-dependent DNA binding activity and a
DNA-dependent ATPase. However, this reaction is less
efficient and requires accessory proteins such as
RAD55/57 ..
Length = 235
Score = 30.2 bits (68), Expect = 1.0
Identities = 23/112 (20%), Positives = 43/112 (38%), Gaps = 13/112 (11%)
Query: 179 IVAPPRTGKTILLQNIAHSIKKNHPECYLI----VLLIDE----RPEEVTDMQRS---VQ 227
I +GKT L +A +++ P + ID RPE + +
Sbjct: 24 IFGEFGSGKTQLCHQLAVTVQ--LPIELGGLEGKAVYIDTEGTFRPERLVQIAERFGLDP 81
Query: 228 GEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNV 279
EV+ + + A +++ L+E ++++DS+T L RA
Sbjct: 82 EEVLDNIYVARAYNSDHQLQLLEELEAILIESSRIKLVIVDSVTALFRAEFD 133
>gnl|CDD|31673 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 30.4 bits (68), Expect = 1.1
Identities = 14/61 (22%), Positives = 25/61 (40%)
Query: 148 FNMELNNPENKDISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYL 207
F+ E +K + L+ +G+ +++ PP GKT L I + + K
Sbjct: 79 FDFEFQPGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLF 138
Query: 208 I 208
I
Sbjct: 139 I 139
>gnl|CDD|33644 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 29.6 bits (66), Expect = 1.7
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 5/43 (11%)
Query: 178 LIVAPPRTGKTILLQNIAHSI---KKNHPECYLIVLLIDERPE 217
LI+ PP+ GKT LL++IA + V +IDER E
Sbjct: 141 LIIGPPQVGKTTLLRDIARLLSDGINQFL--PKKVGIIDERSE 181
>gnl|CDD|144153 pfam00450, Peptidase_S10, Serine carboxypeptidase.
Length = 415
Score = 29.2 bits (66), Expect = 2.0
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 130 VRNKIHFDNLTPLYPDKRFNMELNNPENKDISSRVIDLIAP-IGKGQRSLIVA 181
V+ +H N+ + R N E+NN DIS ++ ++ + G R LI +
Sbjct: 286 VQKALHA-NVGSVGEWSRCNDEVNNWYGDDISKSMLPILPKLLEGGLRVLIYS 337
>gnl|CDD|31261 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 29.3 bits (65), Expect = 2.1
Identities = 15/66 (22%), Positives = 26/66 (39%), Gaps = 4/66 (6%)
Query: 136 FDNLTPLYPDKRFNMELNNPENKDISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIA 195
D PL F EL + + + L+ +R +IV P GKT++
Sbjct: 21 LDEGLPLKLIVAFEFELRPYQEEALD----ALVKNRRTERRGVIVLPTGAGKTVVAAEAI 76
Query: 196 HSIKKN 201
+K++
Sbjct: 77 AELKRS 82
>gnl|CDD|37013 KOG1802, KOG1802, KOG1802, RNA helicase nonsense mRNA reducing
factor (pNORF1) [RNA processing and modification].
Length = 935
Score = 29.2 bits (65), Expect = 2.5
Identities = 33/164 (20%), Positives = 64/164 (39%), Gaps = 3/164 (1%)
Query: 40 SILKVLSGRDVEIIGEGVIEVLQDGFGF-LRSPDANYLAGPDDIYVSPSQIKSFSLKTGD 98
S LK+ G ++ + G + + +G G L+ PD N + + SQ + G
Sbjct: 292 SELKLAIGDEIRLTYSGGLVLPWNGIGSVLKIPDNNGDE--VKLELEFSQDPPIEVTHGF 349
Query: 99 TVEGSIRAPREGERYFALLKVNAINFDVPERVRNKIHFDNLTPLYPDKRFNMELNNPENK 158
TV+ ++ AL + V + +K+ + K + P
Sbjct: 350 TVDFVWKSTSFDRMQLALKLLAVDEKKVSGYLYHKLLGHPVEDSSLKKLLPRRFSVPNLP 409
Query: 159 DISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNH 202
+++ + + + + SLI PP TGKT+ I + + + H
Sbjct: 410 KLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQH 453
>gnl|CDD|37017 KOG1806, KOG1806, KOG1806, DEAD box containing helicases
[Replication, recombination and repair].
Length = 1320
Score = 28.0 bits (62), Expect = 4.7
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 177 SLIVAPPRTGKTILLQNIAHSIKKNHPE 204
+++V PP TGKT + I + N P
Sbjct: 756 TMVVGPPGTGKTDVAVQILSVLYHNSPN 783
>gnl|CDD|36567 KOG1353, KOG1353, KOG1353, F0F1-type ATP synthase, alpha subunit
[Energy production and conversion].
Length = 340
Score = 27.6 bits (61), Expect = 6.1
Identities = 29/104 (27%), Positives = 42/104 (40%), Gaps = 13/104 (12%)
Query: 96 TGDTVEGSIRAPREGERYFALLKVNAINFDVP------ERVRNKI--HFDNLTPLYPDKR 147
G V G +EG+ K A DVP RV + D + +R
Sbjct: 64 VGVVVFGEDSLIKEGDTV----KRTAAISDVPPLKALLGRVGCALGEPIDGNGKISAKER 119
Query: 148 FNMELNN-PENKDISSRVIDLIAPIGKGQRSLIVAPPRTGKTIL 190
+ + E + +D + PIG+GQR LI+ +TGKT L
Sbjct: 120 RIIPRASVDEPMQTGLKAVDSLVPIGRGQRELIIGDRQTGKTSL 163
>gnl|CDD|35950 KOG0731, KOG0731, KOG0731, AAA+-type ATPase containing the
peptidase M41 domain [Posttranslational modification,
protein turnover, chaperones].
Length = 774
Score = 27.7 bits (61), Expect = 6.2
Identities = 24/68 (35%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 132 NKIHFDNLTPLYPDKRFNME----LNNPENKDISSRVIDLIAPIGKGQRSLIVAPPRTGK 187
+ F ++ + K ME L NPE + +L A I KG L+V PP TGK
Sbjct: 306 TGVKFKDVAGVDEAKEELMEFVKFLKNPE------QYQELGAKIPKG--VLLVGPPGTGK 357
Query: 188 TILLQNIA 195
T+L + IA
Sbjct: 358 TLLAKAIA 365
>gnl|CDD|31232 COG1029, FwdB, Formylmethanofuran dehydrogenase subunit B [Energy
production and conversion].
Length = 429
Score = 27.6 bits (61), Expect = 6.6
Identities = 20/69 (28%), Positives = 27/69 (39%), Gaps = 8/69 (11%)
Query: 170 PIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLI-------DERPEEVTDM 222
P G+ R++IV PR T L + IK N + LI L R EEV +
Sbjct: 172 PRGREDRTVIVVDPRKTATAKLADNHVQIKPNS-DYELISALRAALHGKEPHRSEEVAGV 230
Query: 223 QRSVQGEVI 231
E+
Sbjct: 231 PIEEIEELA 239
>gnl|CDD|48410 cd02412, 30S_S3_KH, K homology RNA-binding (KH) domain of the
prokaryotic 30S small ribosomal subunit protein S3. S3
is part of the head region of the 30S ribosomal subunit
and is believed to interact with mRNA as it threads its
way from the latch into the channel. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In general, KH
binds single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA..
Length = 109
Score = 27.7 bits (62), Expect = 6.8
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 334 IFEEFKGTGNSEIVLERKIADKRI-----FPAMDIIKSGTRKEDLLVERQDLQKVFMLRR 388
I ++ K G S I +ERK + P + I K G E L R++LQK+ ++
Sbjct: 42 IKKKLKKAGISRIEIERKADRVEVTIHTARPGIIIGKKGAGIEKL---RKELQKLLGNKK 98
Query: 389 I 389
+
Sbjct: 99 V 99
>gnl|CDD|35954 KOG0735, KOG0735, KOG0735, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 952
Score = 27.7 bits (61), Expect = 7.2
Identities = 8/37 (21%), Positives = 18/37 (48%)
Query: 166 DLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNH 202
++P+ + L+ P +GKT L++ + K+
Sbjct: 423 QELSPVFRHGNILLNGPKGSGKTNLVKALFDYYSKDL 459
>gnl|CDD|30903 COG0557, VacB, Exoribonuclease R [Transcription].
Length = 706
Score = 27.3 bits (60), Expect = 8.9
Identities = 24/115 (20%), Positives = 46/115 (40%), Gaps = 15/115 (13%)
Query: 10 KNKSPTKLLAFAESLEIENANVMRKQELMFSILKV----------LSGRDVEIIGEGVIE 59
+++ P A++L +E V + L+ ++ + + + EG++E
Sbjct: 16 ESEDPLSRKELAKALGLEGEEVEDLRRLLRALEREGQLLKKRRGRYLLPEELDLVEGIVE 75
Query: 60 VLQDGFGFLRSPDANYLAGPDDIYVSPSQIKSFSLKTGDTVEGSIRAPREGERYF 114
GFGFL D+ DDI+V + +L GD V + + R+
Sbjct: 76 ASAKGFGFLSPDDSKD---ADDIFVPKDPLN-RALH-GDRVLVELLPSDKRGRFK 125
>gnl|CDD|35947 KOG0728, KOG0728, KOG0728, 26S proteasome regulatory complex,
ATPase RPT6 [Posttranslational modification, protein
turnover, chaperones].
Length = 404
Score = 27.3 bits (60), Expect = 8.9
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 5/31 (16%)
Query: 178 LIVAPPRTGKTILLQNIAHSIKKNHPECYLI 208
L+ PP TGKT+L + +AH H +C I
Sbjct: 185 LLYGPPGTGKTLLARAVAH-----HTDCTFI 210
>gnl|CDD|163681 cd07943, DRE_TIM_HOA, 4-hydroxy-2-oxovalerate aldolase, N-terminal
catalytic TIM barrel domain. 4-hydroxy 2-ketovalerate
aldolase (Also known as 4-hydroxy-2-ketovalerate
aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA))
converts 4-hydroxy-2-oxopentanoate to acetaldehyde and
pyruvate, the penultimate step in the meta-cleavage
pathway for the degradation of phenols, cresols and
catechol. This family includes the Escherichia coli
MhpE aldolase, the Pseudomonas DmpG aldolase, and the
Burkholderia xenovorans BphI pyruvate aldolase. In
Pseudomonas, the DmpG aldolase tightly associates with a
dehydrogenase (DmpF ) and is inactive without it. HOA
has a canonical TIM-barrel fold with a C-terminal
extension that forms a funnel leading to the active
site. This family belongs to the DRE-TIM metallolyase
superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 263
Score = 27.1 bits (61), Expect = 9.1
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 242 HVQVAEMVIAKAKCLVEYGLDVVILLDS 269
H+ E + +AK + YG D V + DS
Sbjct: 136 HMASPEELAEQAKLMESYGADCVYVTDS 163
>gnl|CDD|177079 CHL00174, accD, acetyl-CoA carboxylase beta subunit; Reviewed.
Length = 296
Score = 27.2 bits (61), Expect = 9.4
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 393 MNSSDAIEFLIDK 405
M+SSD IE LID
Sbjct: 69 MSSSDRIELLIDP 81
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.318 0.136 0.375
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,963,986
Number of extensions: 272421
Number of successful extensions: 823
Number of sequences better than 10.0: 1
Number of HSP's gapped: 804
Number of HSP's successfully gapped: 62
Length of query: 423
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 327
Effective length of database: 4,189,273
Effective search space: 1369892271
Effective search space used: 1369892271
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.5 bits)