Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_013835422.1 THICY_RS04490 acetate--CoA ligase
Query= SwissProt::P31638
(660 letters)
>NCBI__GCF_000214825.1:WP_013835422.1
Length = 651
Score = 831 bits (2146), Expect = 0.0
Identities = 402/656 (61%), Positives = 503/656 (76%), Gaps = 9/656 (1%)
Query: 4 IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63
IES++ E RVF P + QAAI + + A+ +AE+D+ GFWA A+E L W KPFTK
Sbjct: 5 IESILTETRVFEPSDAIKQQAAIKA-DKLDAMYAKAEQDHVGFWADLAKEKLSWHKPFTK 63
Query: 64 VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123
LD S AP Y+WF DGELN SYNC+DR+L +DK+AI+FE D G V TY+ELH +V
Sbjct: 64 ALDDSKAPLYRWFTDGELNVSYNCIDRHLDT-KSDKLAIIFEGDKGDVHHYTYQELHDEV 122
Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183
CRFAN LK GI++GDRV+IYMPM + V+AMQACAR+GA HSVVFGGFSA++L++R+ +
Sbjct: 123 CRFANTLKTQGIKQGDRVIIYMPMIPQAVIAMQACARVGAIHSVVFGGFSAEALKDRVEN 182
Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243
A +IT D +RGGKA+PLK D ALA G C++V+ VIVY+RT +V +GRD W
Sbjct: 183 AAAKLIITTDGGLRGGKAIPLKGAVDQALAKG-CDSVKKVIVYQRTKQEVVMQDGRDIWW 241
Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303
+ AG + + + A+HPLF+LYTSGSTG PKGVQH +GGYLL A++T +W FD+
Sbjct: 242 HEAEAGMSNYHDPVMLPADHPLFLLYTSGSTGTPKGVQHGSGGYLLNAMLTNEWMFDLND 301
Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363
D+FWCTAD+GW+TGH+Y+AYGPLA GAT V+FEGVPTYP+AGRFW + H V++FYTA
Sbjct: 302 KDVFWCTADVGWITGHSYVAYGPLAMGATIVMFEGVPTYPDAGRFWQVCQDHGVTVFYTA 361
Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423
PTAIR+L+K K P QYDLS LR+LGTVGEPINPEAWMWY++ IG CPI+DT+
Sbjct: 362 PTAIRALMKFG----KDIPAQYDLSKLRILGTVGEPINPEAWMWYHEVIGRGECPIIDTW 417
Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAM 483
WQTETG HMI P PG TPL PGSCT PLPGI A +VDE GH++ N +GG LVV++PWP+M
Sbjct: 418 WQTETGAHMIAPFPGVTPLKPGSCTRPLPGIDAIVVDEEGHEIGNNSGGYLVVRKPWPSM 477
Query: 484 IRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTM 543
++T+WGD +R+ +YF + + Y+ GD + +D D GY I+GRIDDVLNVSGHR+GTM
Sbjct: 478 LQTVWGDDQRYIDTYF-AKFNNQYYVVGDSAHKDAD-GYIWILGRIDDVLNVSGHRLGTM 535
Query: 544 EIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEI 603
EIESALV++P VAEAAVVG+P D+ GE++ AFVVL P G E + ELRNWV +EI
Sbjct: 536 EIESALVAHPKVAEAAVVGKPHDVKGESVFAFVVLNTDLPAGAERDAMVNELRNWVAQEI 595
Query: 604 GPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659
GPIAKP DIRFG NLPKTRSGKIMRRLLR++AKGEEITQDTSTLE+P+IL+QL+QA
Sbjct: 596 GPIAKPDDIRFGTNLPKTRSGKIMRRLLRTIAKGEEITQDTSTLEDPSILKQLQQA 651
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: 1304
Number of extensions: 64
Number of successful extensions: 6
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: 651
Length adjustment: 38
Effective length of query: 622
Effective length of database: 613
Effective search space: 381286
Effective search space used: 381286
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_013835422.1 THICY_RS04490 (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.18710.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.9e-306 1002.7 0.1 3.3e-306 1002.5 0.1 1.0 1 lcl|NCBI__GCF_000214825.1:WP_013835422.1 THICY_RS04490 acetate--CoA ligas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214825.1:WP_013835422.1 THICY_RS04490 acetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1002.5 0.1 3.3e-306 3.3e-306 3 628 .. 28 650 .. 26 651 .] 0.98
Alignments for each domain:
== domain 1 score: 1002.5 bits; conditional E-value: 3.3e-306
TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvekrk 71
++++ ++y++a++d+ fwa+lake+l+w+kpf+k ld+s++p ++Wf+dgelnvsync+drh+ +++
lcl|NCBI__GCF_000214825.1:WP_013835422.1 28 KADKLDAMYAKAEQDHVGFWADLAKEKLSWHKPFTKALDDSKAPLYRWFTDGELNVSYNCIDRHLDTKS 96
5678899************************************************************** PP
TIGR02188 72 dkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGav 140
dk+aii+egd +g d++++tY+el++evcr+an+lk++G+k+gdrv+iY+pmip+aviam+acaR+Ga+
lcl|NCBI__GCF_000214825.1:WP_013835422.1 97 DKLAIIFEGD-KG-DVHHYTYQELHDEVCRFANTLKTQGIKQGDRVIIYMPMIPQAVIAMQACARVGAI 163
**********.55.59***************************************************** PP
TIGR02188 141 hsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeeva 209
hsvvf+Gfsaeal++R+++a akl+it+d+glRggk+i+lk +vd+al+k +sv+kv+v++rt++ev+
lcl|NCBI__GCF_000214825.1:WP_013835422.1 164 HSVVFGGFSAEALKDRVENAAAKLIITTDGGLRGGKAIPLKGAVDQALAKGCDSVKKVIVYQRTKQEVV 232
*************************************************9999**************88 PP
TIGR02188 210 ewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdi 278
+++grD+ww+e+ + + s++++p l +++plf+LYtsGstG+PkGv+h +gGyll a+lt +++fd+
lcl|NCBI__GCF_000214825.1:WP_013835422.1 233 -MQDGRDIWWHEAEA-GMSNYHDPVMLPADHPLFLLYTSGSTGTPKGVQHGSGGYLLNAMLTNEWMFDL 299
.************99.6**************************************************** PP
TIGR02188 279 kdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRal 347
+d+d+fwCtaDvGW+tGhsY+ ygPLa+Gat ++fegvptypda+rfw+v++ ++vt+fYtaPtaiRal
lcl|NCBI__GCF_000214825.1:WP_013835422.1 300 NDKDVFWCTADVGWITGHSYVAYGPLAMGATIVMFEGVPTYPDAGRFWQVCQDHGVTVFYTAPTAIRAL 368
********************************************************************* PP
TIGR02188 348 mklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatel 416
mk g+++++++dls+lr+lg+vGepinpeaw+Wy+ev+G+++cpi+dtwWqtetG+++i+p+pg +t+l
lcl|NCBI__GCF_000214825.1:WP_013835422.1 369 MKFGKDIPAQYDLSKLRILGTVGEPINPEAWMWYHEVIGRGECPIIDTWWQTETGAHMIAPFPG-VTPL 436
****************************************************************.5*** PP
TIGR02188 417 kpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg.lyftG 484
kpgs+t+Pl+Gi+a vvdeeg+e+ ++++ g+Lv++kpwPsml+t++gd++r+++tYf k+++ +y G
lcl|NCBI__GCF_000214825.1:WP_013835422.1 437 KPGSCTRPLPGIDAIVVDEEGHEIGNNSG-GYLVVRKPWPSMLQTVWGDDQRYIDTYFAKFNNqYYVVG 504
**************************999.8******************************9868889* PP
TIGR02188 485 DgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkeg 553
D+a++d+dGyiwilGR+Ddv+nvsGhrlgt+eiesalv+h++vaeaavvg+p+++kge+++afvvl++
lcl|NCBI__GCF_000214825.1:WP_013835422.1 505 DSAHKDADGYIWILGRIDDVLNVSGHRLGTMEIESALVAHPKVAEAAVVGKPHDVKGESVFAFVVLNTD 573
*******************************************************************99 PP
TIGR02188 554 veedee..elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledp 620
+ +e ++ +el+++v++eigpiakpd+i++ ++lPktRsGkimRRllr+ia+gee+++d+stledp
lcl|NCBI__GCF_000214825.1:WP_013835422.1 574 LPAGAErdAMVNELRNWVAQEIGPIAKPDDIRFGTNLPKTRSGKIMRRLLRTIAKGEEITQDTSTLEDP 642
886555448************************************************************ PP
TIGR02188 621 svveelke 628
s++++l++
lcl|NCBI__GCF_000214825.1:WP_013835422.1 643 SILKQLQQ 650
*****987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (651 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.75
//
[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