RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254781049|ref|YP_003065462.1| succinyl-CoA synthetase
subunit beta [Candidatus Liberibacter asiaticus str. psy62]
(398 letters)
>2nu8_B SCS-beta, succinyl-COA synthetase beta chain; citric acid cycle,
heterotetramer, ligase, ATP-grAsp fold, rossmann fold;
HET: COA; 2.15A {Escherichia coli} SCOP: c.23.4.1
d.142.1.4 PDB: 1scu_B* 2nu6_B* 1jkj_B* 2nu7_B* 2nu9_B*
2nua_B* 2scu_B* 1jll_B* 1cqj_B* 1cqi_B*
Length = 388
Score = 411 bits (1058), Expect = e-115
Identities = 196/397 (49%), Positives = 265/397 (66%), Gaps = 10/397 (2%)
Query: 1 MNIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFK 60
MN+HEYQAK L +Y +P G ++ AE A + +VVK Q+HAGGRGK
Sbjct: 1 MNLHEYQAKQLFARYGLPAPVGYACTTPREAEEAASKIGAGPWVVKCQVHAGGRGKA--- 57
Query: 61 ELPADSKGGVRVESSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYL 120
GGV+V +S + + + LG L+T QT G VN + VE DI +ELYL
Sbjct: 58 -------GGVKVVNSKEDIRAFAENWLGKRLVTYQTDANGQPVNQILVEAATDIAKELYL 110
Query: 121 SLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVTSEDVASLCDMLELQ 180
+VDR+S V F+AST+GG++IE+VA++ P I K+ +DPL G L L L+
Sbjct: 111 GAVVDRSSRRVVFMASTEGGVEIEKVAEETPHLIHKVALDPLTGPMPYQGRELAFKLGLE 170
Query: 181 GQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALYRHLDIQ 240
G+ +F L F ++D++L+EINPL+I K G L LD K+ D NAL+R D++
Sbjct: 171 GKLVQQFTKIFMGLATIFLERDLALIEINPLVITKQGDLICLDGKLGADGNALFRQPDLR 230
Query: 241 ELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVG 300
E+RD S+ED RE +A Q L+Y+ALDGNIGCMVNGAGLAM TMDI+KL+GG PANFLDVG
Sbjct: 231 EMRDQSQEDPREAQAAQWELNYVALDGNIGCMVNGAGLAMGTMDIVKLHGGEPANFLDVG 290
Query: 301 GGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE 360
GGA +++V AFKII SD VK +L+NIFGGI+RCD++ GI+ AV EV +N+P+V+RLE
Sbjct: 291 GGATKERVTEAFKIILSDDKVKAVLVNIFGGIVRCDLIADGIIGAVAEVGVNVPVVVRLE 350
Query: 361 GANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG 397
G N ++G + +A+SGLN+I A L DAAQ++V AV+G
Sbjct: 351 GNNAELGAKKLADSGLNIIAAKGLTDAAQQVVAAVEG 387
>2fp4_B Succinyl-COA ligase [GDP-forming] beta-chain, mitochondrial; active
site phosphohistidine residue; HET: NEP GTP; 2.08A {Sus
scrofa} SCOP: c.23.4.1 d.142.1.4 PDB: 2fpg_B* 2fpi_B*
2fpp_B* 1euc_B* 1eud_B*
Length = 395
Score = 373 bits (959), Expect = e-104
Identities = 171/397 (43%), Positives = 237/397 (59%), Gaps = 3/397 (0%)
Query: 1 MNIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFK 60
MN+ EYQ+K L+ V V + V + + A A K L V+K+QI AGGRGKG F
Sbjct: 1 MNLQEYQSKKLMSDNGVKVQRFFVADTANEALEAAKRLNAKEIVLKAQILAGGRGKGVFS 60
Query: 61 ELPADSKGGVRVESSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYL 120
KGGV + + V ++++G L TKQT G +VN V V + DI RE YL
Sbjct: 61 S---GLKGGVHLTKDPEVVGQLAKQMIGYNLATKQTPKEGVKVNKVMVAEALDISRETYL 117
Query: 121 SLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVTSEDVASLCDMLELQ 180
++L+DR+ + S QGG+DIEEVA P+ IFK ID + G+ + + L
Sbjct: 118 AILMDRSCNGPVLVGSPQGGVDIEEVAASNPELIFKEQIDIIEGIKDSQAQRMAENLGFL 177
Query: 181 GQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALYRHLDIQ 240
G + D LY F D + +E+NP G++ D+KI+FDDNA +R DI
Sbjct: 178 GPLQNQAADQIKKLYNLFLKIDATQVEVNPFGETPEGQVVCFDAKINFDDNAEFRQKDIF 237
Query: 241 ELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVG 300
+ D SE + E EA +++L YI LDGNI C VNGAGLAMAT DII L GG PANFLD+G
Sbjct: 238 AMDDKSENEPIENEAAKYDLKYIGLDGNIACFVNGAGLAMATCDIIFLNGGKPANFLDLG 297
Query: 301 GGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE 360
GG + +V AFK++T+D V+ IL+NIFGGI+ C ++ GI A +E+++ +PLV+RLE
Sbjct: 298 GGVKESQVYQAFKLLTADPKVEAILVNIFGGIVNCAIIANGITKACRELELKVPLVVRLE 357
Query: 361 GANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG 397
G NV ++ SGL + +A+DL+DAA+K V +V
Sbjct: 358 GTNVHEAQNILTNSGLPITSAVDLEDAAKKAVASVTK 394
>3mwd_A ATP-citrate synthase; ATP-grAsp, phosphohistidine, organic acid,
lyase, transferas; HET: CIT; 2.10A {Homo sapiens} PDB:
3mwe_A*
Length = 425
Score = 288 bits (737), Expect = 2e-78
Identities = 83/436 (19%), Positives = 137/436 (31%), Gaps = 58/436 (13%)
Query: 1 MNIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKT---------LPGPLYVVKSQIHA 51
I E K LL K+ + L VVK
Sbjct: 4 KAISEQTGKELLYKFICTTSAIQNRFKYARVTPDTDWARLLQDHPWLLSQNLVVKPDQLI 63
Query: 52 GGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDG 111
RGK G V V +L V S ++ LG G + +E
Sbjct: 64 KRRGKL----------GLVGVNLTLDGVKSWLKPRLGQE---ATVGKATGFLKNFLIEPF 110
Query: 112 ADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVTSEDVA 171
+ + + T + +GG+D+ +V + + +D +
Sbjct: 111 VPHSQAEEFYVCIYATREGDYVLFHHEGGVDVGDVDAKAQKLLVG--VDEKLNPEDIKKH 168
Query: 172 SLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDN 231
L E + + L+ + D + LEINPL++ K+G + VLD D
Sbjct: 169 LLVHAPEDKKEILA---SFISGLFNFYEDLYFTYLEINPLVVTKDG-VYVLDLAAKVDAT 224
Query: 232 ALYRHLDIQELRDVSEEDSRE-------------IEAKQHNLSYIALDGNIGCMVNGAGL 278
A Y + RE L+ + G I MV G G
Sbjct: 225 ADYICKVKWGDIEFPPPFGREAYPEEAYIADLDAKSGASLKLTLLNPKGRIWTMVAGGGA 284
Query: 279 AMATMDIIKLYGGA--PANFLDVGGGADQDKVAA----AFKIITSDSSVKGILINIFGGI 332
++ D I GG AN+ + G + + ++T + G ++ I G I
Sbjct: 285 SVVYSDTICDLGGVNELANYGEYSGAPSEQQTYDYAKTILSLMTREKHPDGKILIIGGSI 344
Query: 333 MRCDVL---VKGILSAVKEVK-----INIPLVMRLEGANVDIGNRLIAESGLNV---ITA 381
+ KGI+ A+++ + + + +R G N G R++ E G I
Sbjct: 345 ANFTNVAATFKGIVRAIRDYQGPLKEHEVTIFVRRGGPNYQEGLRVMGEVGKTTGIPIHV 404
Query: 382 IDLDDAAQKIVHAVKG 397
+ IV G
Sbjct: 405 FGTETHMTAIVGMALG 420
>1wr2_A Hypothetical protein PH1789; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
2.00A {Pyrococcus horikoshii OT3}
Length = 238
Score = 111 bits (279), Expect = 3e-25
Identities = 35/233 (15%), Positives = 78/233 (33%), Gaps = 19/233 (8%)
Query: 3 IHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKEL 62
+ EY+AK +L+ Y +PV + + ++ A K + P+ + + + L
Sbjct: 20 MVEYEAKQVLKAYGLPVPEEKLAKTLDEALEYAKEIGYPVVLKLMSPQILHKSDAKVVML 79
Query: 63 PADSKGGVRVESSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSL 122
++++ + + + V V RE+ + +
Sbjct: 80 N-------------IKNEEELKKKWEEIHENAKKYRPDAEILGVLVAPMLKPGREVIIGV 126
Query: 123 LVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVTSEDVASLCDMLELQGQ 182
D G I GG+ +E + + + D + + +
Sbjct: 127 TEDPQFGH--AIMFGLGGIFVEILKDVTFRLVPITEKDARKMIQEIKAYPILAGARGEEP 184
Query: 183 ARIDG-GDLFPNLYKAFCDKD--MSLLEINPLIIMKNG-RLRVLDSKISFDDN 231
A ID D+ + K D + +++NP+ + G ++DS+I
Sbjct: 185 ADIDAIVDMLLKVSKLVDDLKDYIKEMDLNPVFVYNKGEGAVIVDSRIILKPK 237
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 70.4 bits (172), Expect = 6e-13
Identities = 77/515 (14%), Positives = 146/515 (28%), Gaps = 211/515 (40%)
Query: 2 NIHEYQAKALL--RKYNVPVAKGVVISSVHAAESAIKTLPGP----LYVV----KSQIHA 51
+IH A LL + K ++ + + A A + L+ +Q+ A
Sbjct: 100 DIHAL-AAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVA 158
Query: 52 --GGRGKGR--FKELPADSKGGVRVE--SSLKSVISDIREILGSTLITKQTGPTGSRVNC 105
GG+G F+EL + + ++ D+ + TL
Sbjct: 159 IFGGQGNTDDYFEEL---------RDLYQTYHVLVGDLIKFSAETLSELIRTT--LDAEK 207
Query: 106 VYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLID-PLIG 164
V+ + G +IL +L T ++ S P I PLIG
Sbjct: 208 VFTQ-GLNILE--WLENP-SNTPD-KDYLLSI-------------P-------ISCPLIG 242
Query: 165 VTSEDVASLC--------------DMLE-LQG-----Q-----ARIDGGDLFPNLYKAFC 199
V L ++ L+G Q I D + + + +
Sbjct: 243 VI-----QLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSV- 296
Query: 200 DKDMSLL--------------EINPLII---MKNGR------LRVLDSKISFDDNALYRH 236
K +++L + P I+ ++N L + + + +
Sbjct: 297 RKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQE----QVQDY 352
Query: 237 LDI--QELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNG------AGLAMATMDIIKL 288
++ L + + I+L VNG +G + L
Sbjct: 353 VNKTNSHLP----AGKQ-V--------EISL-------VNGAKNLVVSGPPQS------L 386
Query: 289 YG--------GAPANFLDVGGGADQDKV-------------------------AAAFKII 315
YG AP+ G DQ ++ A +I
Sbjct: 387 YGLNLTLRKAKAPS-------GLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLI 439
Query: 316 TSDSSVKGILIN-------IF----GGIMR--CDVLVKGILSAVKEVKINIPLVMRLE-- 360
D + N ++ G +R + + I+ + + + + +
Sbjct: 440 NKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKAT 499
Query: 361 -------GANVDIG---NRLIAESGLNVITAIDLD 385
G +G +R +G+ VI A LD
Sbjct: 500 HILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLD 534
>3lxq_A Uncharacterized protein VP1736; alkaline, phosphatase, MDOB,
sulfatase, PSI, MCSG, structural genomics; 1.95A {Vibrio
parahaemolyticus}
Length = 450
Score = 32.8 bits (74), Expect = 0.16
Identities = 14/101 (13%), Positives = 39/101 (38%), Gaps = 13/101 (12%)
Query: 165 VTSEDVA-SLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLD 223
+ D+ +L ++ + + + G DL L + + + ++++ + KN D
Sbjct: 341 ANNIDMPPTLLSLIGVDAKTPMIGRDLTKPLAR---EDERAMMQYD-----KNFGYLTRD 392
Query: 224 SKISFDDNALYRH----LDIQELRDVSEEDSREIEAKQHNL 260
+ + + Q ++ + ++S AK + L
Sbjct: 393 NLVVLSPGEKVSTMEYDFESQTMKPLEVDESVIDRAKANAL 433
>3lp8_A Phosphoribosylamine-glycine ligase; ssgcid, NIH, niaid, SBRI, UW,
emerald biostructures, ALS collaborative
crystallography; 2.15A {Ehrlichia chaffeensis}
Length = 442
Score = 32.3 bits (73), Expect = 0.19
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRG 55
K L +Y +P AK ++A I P VVK+ A G+G
Sbjct: 128 KELCMRYGIPTAKYGYFVDTNSAYKFIDKHKLP-LVVKADGLAQGKG 173
>3hbl_A Pyruvate carboxylase; TIM barrel, ligase; HET: BTI ADP; 2.71A
{Staphylococcus aureus subsp} PDB: 3bg5_A* 3ho8_A*
3hb9_A*
Length = 1150
Score = 30.8 bits (69), Expect = 0.53
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 7 QAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRG 55
+A+ K ++PV G I S A+ + PL ++K+ GG+G
Sbjct: 121 KARTTAIKADLPVIPGTDGPIKSYELAKEFAEEAGFPL-MIKATSGGGGKG 170
>2ra9_A Uncharacterized protein DUF1285; YP_001050848.1, protein of unknown
function DUF1285, structural genomics; 1.40A {Shewanella
baltica OS155}
Length = 150
Score = 29.9 bits (67), Expect = 1.1
Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 7/87 (8%)
Query: 163 IGVTSEDVA-SLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRV 221
+ V ED + D Q + ++ L+ K M L + + + ++ G
Sbjct: 70 VRVQVEDAPLLIVDFERAQPHSLLNVSTSIGTLHHNVDIKQMKLTDDSVYLPLERG---- 125
Query: 222 LDSKISFDDNALYRHLDIQELRDVSEE 248
L K+ Y ++ L D++E+
Sbjct: 126 LWGKLG--RACYYNFVNEFNLSDLNEQ 150
>2qf7_A Pyruvate carboxylase protein; multi-domain, multi-functional,
biotin-dependent, ligase; HET: KCX COA SAP; 2.00A
{Rhizobium etli cfn 42}
Length = 1165
Score = 29.3 bits (65), Expect = 1.4
Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 5/53 (9%)
Query: 7 QAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKG 57
A+ L VPV + + + P+ ++K+ GG G+G
Sbjct: 137 AARNLAISVGVPVVPATEPLPDDMAEVAKMAAAIGYPV-MLKAS--WGGGGRG 186
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.2 bits (64), Expect = 1.6
Identities = 6/23 (26%), Positives = 12/23 (52%), Gaps = 4/23 (17%)
Query: 307 KVAAAFKIITSDS----SVKGIL 325
K+ A+ K+ DS ++K +
Sbjct: 24 KLQASLKLYADDSAPALAIKATM 46
>1vav_A Alginate lyase PA1167; beta-sandwich, structural genomics; 2.00A
{Pseudomonas aeruginosa PAO1} SCOP: b.29.1.18
Length = 222
Score = 28.4 bits (63), Expect = 2.7
Identities = 13/59 (22%), Positives = 24/59 (40%)
Query: 9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSK 67
+A LR VP + ++I +H+ S + ++ GR + +E P D
Sbjct: 83 EATLRIEAVPSTRRMIIGQIHSDGSNSGQAAPLVKLLYQLRLDQGRVQALVRERPDDGG 141
>2ve7_C Kinetochore protein NUF2, kinetochore protein SPC24; division
cycle-associated protein...; HEC1, NDC80, nucleus,
mitosis, centromere, cell cycle; 2.88A {Homo sapiens}
Length = 250
Score = 28.3 bits (63), Expect = 3.3
Identities = 16/121 (13%), Positives = 36/121 (29%), Gaps = 10/121 (8%)
Query: 149 DYPQKIFKLLIDPLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEI 208
+ I+ + + G+ E + + ++G F NL D + + +
Sbjct: 48 EVLHMIYMRALQIVYGIRLEHFYMMPVNSGVMYPHLMEGFLPFSNLVTH-LDSFLPICRV 106
Query: 209 NPLIIM-----KNGRLRVLDSKIS----FDDNALYRHLDIQELRDVSEEDSREIEAKQHN 259
N K R S I F + +++ S + +++ A
Sbjct: 107 NDFETADILCPKAKRTSRFLSGIINFIHFREACRETYMEFLWQYKSSADKMQQLNAAHQE 166
Query: 260 L 260
Sbjct: 167 A 167
>3n6r_A Propionyl-COA carboxylase, alpha subunit; protein complex,
biotin-dependent carboxylase, ligase; HET: BTI; 3.20A
{Ruegeria pomeroyi}
Length = 681
Score = 27.2 bits (60), Expect = 6.0
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 7 QAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKG 57
+K + ++ NV G +I A + P+ ++K+ AGG GKG
Sbjct: 118 TSKKIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPV-MIKAS--AGGGGKG 167
>1mgp_A Hypothetical protein TM841; two domain structure with mixed
alpha/beta structures in BOTH domains, structural
genomics; HET: PLM; 2.00A {Thermotoga maritima} SCOP:
c.119.1.1 PDB: 1vpv_A*
Length = 313
Score = 26.9 bits (59), Expect = 8.8
Identities = 27/143 (18%), Positives = 52/143 (36%), Gaps = 21/143 (14%)
Query: 99 TGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIAS--TQGGMDIEEVAKDYPQKIFK 156
+G+ + V DI + +LL + A +A + G IEEV K +++
Sbjct: 121 SGTYNSAVLASKEVDIPVYVVDTLLASGAIPLPARVAREMLENGATIEEVLKKLDERMKN 180
Query: 157 LLIDPLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKN 216
+ V+ + L R+ + F +LL+I + ++N
Sbjct: 181 KDFKAIFYVS--------NFDYLVKGGRVSKF-------QGFV---GNLLKIRVCLHIEN 222
Query: 217 GRLRVLDSKISFDDNALYRHLDI 239
G L K+ D A+ ++
Sbjct: 223 GELIPYR-KVRGDKKAIEALIEK 244
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.319 0.138 0.385
Gapped
Lambda K H
0.267 0.0584 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 3,311,085
Number of extensions: 157610
Number of successful extensions: 459
Number of sequences better than 10.0: 1
Number of HSP's gapped: 436
Number of HSP's successfully gapped: 17
Length of query: 398
Length of database: 5,693,230
Length adjustment: 94
Effective length of query: 304
Effective length of database: 3,414,294
Effective search space: 1037945376
Effective search space used: 1037945376
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: 58 (26.4 bits)