Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AO356_16045 AO356_16045 acetyl-CoA synthetase
Query= reanno::pseudo5_N2C3_1:AO356_18695
(651 letters)
>FitnessBrowser__pseudo5_N2C3_1:AO356_16045
Length = 645
Score = 820 bits (2119), Expect = 0.0
Identities = 398/640 (62%), Positives = 479/640 (74%), Gaps = 5/640 (0%)
Query: 5 SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63
S YP V + + YK +Y++S+ +P FW EQA R LDW+ P+ TV++ +D
Sbjct: 5 SQYPHADAVRRAAQLSQDEYKRLYKESIEHPSAFWAEQATRFLDWMTPWQTVQR--YDLK 62
Query: 64 HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
+ D WFA G LNVS NC+DRHL RG+Q+AIIWEGD+P+ES ITY++LH VC+ AN
Sbjct: 63 NGDATWFAGGKLNVSANCIDRHLDTRGEQVAIIWEGDNPAESAQITYKKLHNHVCRLANV 122
Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
L+ + V +GD V IYMPMIPEA AMLACTRIGA+HSVVFGGFSP++L RI+D + V
Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTV 182
Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
ITADEGVR G+ IPLK NVD AL + ++ V+V +RT G + W + RD+WY M
Sbjct: 183 ITADEGVRGGRFIPLKRNVDKALES--CPNVSTVLVVERTQGEVGWVEGRDLWYHQAMHD 240
Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + V DY+ EV+WC
Sbjct: 241 MSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDNEVFWC 300
Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
TADVGWVTGHSYIVYGPLANGATTL+FEGVP++P +R +VIDKH+V+I YTAPTA+RA
Sbjct: 301 TADVGWVTGHSYIVYGPLANGATTLIFEGVPSHPSSSRFWQVIDKHQVNIFYTAPTALRA 360
Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
+M G ++ SLRLLGSVGEPINPEAW+WY+ VG++RCPIVDTWWQTETGG+++
Sbjct: 361 LMREGAGPLQETSRKSLRLLGSVGEPINPEAWEWYFNVVGEQRCPIVDTWWQTETGGIML 420
Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
SPL A LKPG ATRP FGV P L+D +G I GA G L I SWPGQ R++YGDH R
Sbjct: 421 SPLVSAPRLKPGCATRPMFGVQPVLLDEVGKEISGAGSGVLAIKSSWPGQIRSVYGDHQR 480
Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
VDTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H +A
Sbjct: 481 MVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDNIA 540
Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
EAAVVG PHD+KGQGIY +VT G E ++ L+ EL V KEIG A P++IQWAP LP
Sbjct: 541 EAAVVGYPHDLKGQGIYAFVTPMNGVEANDELKKELLAHVSKEIGSFAKPELIQWAPALP 600
Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
KTRSGKIMRRILRKIA E D LGD STLADP VV LI+
Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVEGLID 640
Lambda K H
0.318 0.135 0.418
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: 1350
Number of extensions: 72
Number of successful extensions: 3
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: 651
Length of database: 645
Length adjustment: 38
Effective length of query: 613
Effective length of database: 607
Effective search space: 372091
Effective search space used: 372091
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: 41 (21.7 bits)
S2: 54 (25.4 bits)
Align candidate AO356_16045 AO356_16045 (acetyl-CoA synthetase)
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.26756.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 1027.5 0.0 0 1027.3 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 AO356_16045 acetyl-CoA synthetas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 AO356_16045 acetyl-CoA synthetase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1027.3 0.0 0 0 3 628 .. 20 640 .. 18 641 .. 0.99
Alignments for each domain:
== domain 1 score: 1027.3 bits; conditional E-value: 0
TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvd 64
+++eyk+ly+e+ie+p++fwa++a++ l+w++p+++v++ +l++ +++Wf++g+lnvs+nc+d
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 20 SQDEYKRLYKESIEHPSAFWAEQATRFLDWMTPWQTVQRYDLKNgDATWFAGGKLNVSANCID 82
5799*************************************9999****************** PP
TIGR02188 65 rhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipea 127
rh+ +r ++vaiiwegd++ e s ++tY++l+++vcrlanvlk+ Gvkkgdrv+iY+pmipea
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 83 RHLDTRGEQVAIIWEGDNPAE-SAQITYKKLHNHVCRLANVLKSRGVKKGDRVCIYMPMIPEA 144
*****************9996.***************************************** PP
TIGR02188 128 viamlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealek 190
++amlac+RiGavhsvvf+Gfs+++l++Ri da++++vitadeg+Rgg+ i+lk++vd+ale+
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 145 AYAMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGRFIPLKRNVDKALES 207
*************************************************************** PP
TIGR02188 191 aeesvekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGk 253
++ +v++vlvv+rt+ ev w+egrD+w+++++++ s++c+pe++d+edplfiLYtsGstGk
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 208 CP-NVSTVLVVERTQGEVG-WVEGRDLWYHQAMHD-MSDDCPPEPMDAEDPLFILYTSGSTGK 267
*9.6*************76.**************7.*************************** PP
TIGR02188 254 PkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegv 316
PkGvlhttgGyll+aa+t+kyv d++d+++fwCtaDvGWvtGhsYivygPLanGattl+fegv
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 268 PKGVLHTTGGYLLQAAMTFKYVLDYRDNEVFWCTADVGWVTGHSYIVYGPLANGATTLIFEGV 330
*************************************************************** PP
TIGR02188 317 ptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeawe 379
p++p++srfw+vi+k++v+ifYtaPta+Ralm++g +++++++slr+lgsvGepinpeawe
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 331 PSHPSSSRFWQVIDKHQVNIFYTAPTALRALMREGAGPLQETSRKSLRLLGSVGEPINPEAWE 393
*************************************************************** PP
TIGR02188 380 WyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkevee 442
Wy++vvG+++cpivdtwWqtetGgi+++pl + a lkpg+at+P+fG++++++de gke++
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 394 WYFNVVGEQRCPIVDTWWQTETGGIMLSPLVS-APRLKPGCATRPMFGVQPVLLDEVGKEISG 455
********************************.69**************************98 PP
TIGR02188 443 eeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvi 505
+ gvL+ik++wP+++r++ygd++r+v+tYfk ++g+yftGDgarrd+dG++wi+GR+Ddvi
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 456 AGS-GVLAIKSSWPGQIRSVYGDHQRMVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVI 517
777.8********************************************************** PP
TIGR02188 506 nvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkkl 568
nvsGhr+gtae+esalv h+++aeaavvg+p+++kg+ i+afv+ ++gve+++e l+kel ++
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 518 NVSGHRIGTAEVESALVLHDNIAEAAVVGYPHDLKGQGIYAFVTPMNGVEANDE-LKKELLAH 579
****************************************************95.******** PP
TIGR02188 569 vrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
v+keig++akp+ i+++++lPktRsGkimRR+lrkia +e ++lgd+stl+dpsvve l++
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 580 VSKEIGSFAKPELIQWAPALPKTRSGKIMRRILRKIACNElDSLGDTSTLADPSVVEGLID 640
*********************************************************9876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (645 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 0.02s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 7.91
//
[ok]
This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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