Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_012412490.1 NPUN_RS31835 acetate--CoA ligase
Query= SwissProt::P31638
(660 letters)
>NCBI__GCF_000020025.1:WP_012412490.1
Length = 657
Score = 740 bits (1910), Expect = 0.0
Identities = 371/659 (56%), Positives = 477/659 (72%), Gaps = 13/659 (1%)
Query: 4 IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63
IES++QE+R+F+PP F+ A I S++ Y+ L ++A+ D E FWA A L W + +
Sbjct: 6 IESILQENRLFHPPSEFSQNAHIKSLDDYKRLYEKAKADPEQFWADLAGTELEWFQKWDT 65
Query: 64 VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123
VLD PF KWF G++N SYNCLDR+L +K A+++E + G +TY +LH +V
Sbjct: 66 VLDWQ-PPFAKWFVGGKMNISYNCLDRHLTTWRKNKAALIWEGEPGDSRTLTYAQLHREV 124
Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183
C+FAN LK LG++KGDRV IYMPM E +AM ACAR+GA H VVFGGFSA++L++RL+D
Sbjct: 125 CQFANVLKQLGVQKGDRVGIYMPMIPEAAIAMLACARIGAPHGVVFGGFSAEALRDRLID 184
Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWT-EGRDRW 242
A +ITAD R +PLK D ALA G +V NV+V +RTG + GRD W
Sbjct: 185 ATAKLVITADGGWRKDAIVPLKEQVDKALADGAVPSVENVLVVKRTGQETYMQLGGRDHW 244
Query: 243 MEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIK 302
D+ C AEP+ +E LFVLYTSGSTGKPKGV H+T GY L+ +T KW FD++
Sbjct: 245 WHDLQKSASADCPAEPMDSEDMLFVLYTSGSTGKPKGVVHTTAGYNLYTHITTKWIFDLQ 304
Query: 303 PDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYT 362
D++WCTAD+GW+TGH+YI YGPL+ GAT V++EG P N G FWD+I ++ V+IFYT
Sbjct: 305 DTDVYWCTADVGWITGHSYIVYGPLSNGATTVMYEGAPRASNPGCFWDVIEKYGVNIFYT 364
Query: 363 APTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDT 422
APTAIR+ IK E HP +LSSLRLLGTVGEPINPEAWMWY K IG +RCPIVDT
Sbjct: 365 APTAIRAFIKMGEQ----HPNARNLSSLRLLGTVGEPINPEAWMWYQKVIGGDRCPIVDT 420
Query: 423 FWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPA 482
+WQTETGG MITPLPGA P PGS TLP PGI+A +VD G+ VPN GG L V+ PWP
Sbjct: 421 WWQTETGGIMITPLPGAIPTKPGSATLPFPGIIADVVDLEGNTVPNNEGGYLAVRHPWPG 480
Query: 483 MIRTIWGDPERFRKSYF---PEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHR 539
M+RT++GDPERFR++Y+ P + G Y AGDG+ +D+D GYF +MGR+DDVLNVSGHR
Sbjct: 481 MMRTVYGDPERFRRTYWEHIPPQDGKYTYFAGDGARQDED-GYFWVMGRVDDVLNVSGHR 539
Query: 540 MGTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWV 599
+GTME+ESALVS+P VAEAAVVG+PD++ GE + AFV L+ + EE ++ EL+ V
Sbjct: 540 LGTMEVESALVSHPAVAEAAVVGKPDELKGEEVVAFVTLEGTYQGSEE---LSKELKQHV 596
Query: 600 GKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658
KEIG IA+P +IRF D LPKTRSGKIMRRLLR+LA G+E++ DTSTLE+ ++L++L++
Sbjct: 597 VKEIGAIARPGEIRFTDALPKTRSGKIMRRLLRNLAAGQEVSGDTSTLEDRSVLDKLRE 655
Lambda K H
0.319 0.136 0.422
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1416
Number of extensions: 68
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 660
Length of database: 657
Length adjustment: 38
Effective length of query: 622
Effective length of database: 619
Effective search space: 385018
Effective search space used: 385018
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: 54 (25.4 bits)
Align candidate WP_012412490.1 NPUN_RS31835 (acetate--CoA ligase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR02188.hmm
# target sequence database: /tmp/gapView.20829.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR02188 [M=629]
Accession: TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--CoA ligase
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1025.0 0.0 0 1024.8 0.0 1.0 1 lcl|NCBI__GCF_000020025.1:WP_012412490.1 NPUN_RS31835 acetate--CoA ligase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020025.1:WP_012412490.1 NPUN_RS31835 acetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1024.8 0.0 0 0 2 628 .. 29 655 .. 28 656 .. 0.98
Alignments for each domain:
== domain 1 score: 1024.8 bits; conditional E-value: 0
TIGR02188 2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek. 69
++l++yk+lye+a++dpe+fwa+la +elew++++++vld++ +p++kWf++g++n+sync+drh+++
lcl|NCBI__GCF_000020025.1:WP_012412490.1 29 KSLDDYKRLYEKAKADPEQFWADLAGTELEWFQKWDTVLDWQ-PPFAKWFVGGKMNISYNCLDRHLTTw 96
6899*************************************9.89************************ PP
TIGR02188 70 rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiG 138
rk+k+a+iweg+ +g dsr+ltYa+l+revc++anvlk+lGv+kgdrv iY+pmipea+iamlacaRiG
lcl|NCBI__GCF_000020025.1:WP_012412490.1 97 RKNKAALIWEGE-PG-DSRTLTYAQLHREVCQFANVLKQLGVQKGDRVGIYMPMIPEAAIAMLACARIG 163
************.77.59*************************************************** PP
TIGR02188 139 avhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtge 206
a h vvf+Gfsaeal++R++da+aklvitad+g+R++ +++lk++vd+al++ sve+vlvvkrtg+
lcl|NCBI__GCF_000020025.1:WP_012412490.1 164 APHGVVFGGFSAEALRDRLIDATAKLVITADGGWRKDAIVPLKEQVDKALADGAVpSVENVLVVKRTGQ 232
***************************************************99989************* PP
TIGR02188 207 evaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyv 275
e+ grD+ww++l ++ asa+c++e++dsed+lf+LYtsGstGkPkGv+htt+Gy l++++t+k++
lcl|NCBI__GCF_000020025.1:WP_012412490.1 233 ETYMQLGGRDHWWHDLQKS-ASADCPAEPMDSEDMLFVLYTSGSTGKPKGVVHTTAGYNLYTHITTKWI 300
*8877789**********5.************************************************* PP
TIGR02188 276 fdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtai 344
fd++d+d++wCtaDvGW+tGhsYivygPL+nGatt+++eg+p+ +++++fw+vieky+v+ifYtaPtai
lcl|NCBI__GCF_000020025.1:WP_012412490.1 301 FDLQDTDVYWCTADVGWITGHSYIVYGPLSNGATTVMYEGAPRASNPGCFWDVIEKYGVNIFYTAPTAI 369
********************************************************************* PP
TIGR02188 345 RalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgva 413
Ra++k+ge+++++++lsslr+lg+vGepinpeaw+Wy++v+G ++cpivdtwWqtetGgi+itplpg a
lcl|NCBI__GCF_000020025.1:WP_012412490.1 370 RAFIKMGEQHPNARNLSSLRLLGTVGEPINPEAWMWYQKVIGGDRCPIVDTWWQTETGGIMITPLPG-A 437
*******************************************************************.6 PP
TIGR02188 414 telkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg... 479
+++kpgsatlP++Gi a+vvd eg++v ++e+ g+L++++pwP+m+rt+ygd+erf +tY+++++
lcl|NCBI__GCF_000020025.1:WP_012412490.1 438 IPTKPGSATLPFPGIIADVVDLEGNTVPNNEG-GYLAVRHPWPGMMRTVYGDPERFRRTYWEHIPPqdg 505
*****************************999.8*****************************987788 PP
TIGR02188 480 ..lyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaiva 546
+yf+GDgar+d+dGy+w++GRvDdv+nvsGhrlgt+e+esalvsh+avaeaavvg+pde+kge +va
lcl|NCBI__GCF_000020025.1:WP_012412490.1 506 kyTYFAGDGARQDEDGYFWVMGRVDDVLNVSGHRLGTMEVESALVSHPAVAEAAVVGKPDELKGEEVVA 574
889****************************************************************** PP
TIGR02188 547 fvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvs 615
fv+l+ +++ +e el+kelk++v keig+ia+p +i+++++lPktRsGkimRRllr++a+g+e+ gd+s
lcl|NCBI__GCF_000020025.1:WP_012412490.1 575 FVTLEGTYQGSE-ELSKELKQHVVKEIGAIARPGEIRFTDALPKTRSGKIMRRLLRNLAAGQEVSGDTS 642
*********999.5******************************************************* PP
TIGR02188 616 tledpsvveelke 628
tled+sv+++l+e
lcl|NCBI__GCF_000020025.1:WP_012412490.1 643 TLEDRSVLDKLRE 655
*********9986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (657 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 13.15
//
[ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory