Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate Ga0059261_1313 Ga0059261_1313 acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= reanno::pseudo5_N2C3_1:AO356_18695
(651 letters)
>FitnessBrowser__Korea:Ga0059261_1313
Length = 645
Score = 882 bits (2279), Expect = 0.0
Identities = 422/638 (66%), Positives = 500/638 (78%), Gaps = 3/638 (0%)
Query: 6 LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65
++PV E A D A Y+ +Y +S+ +P FW +QAKRLDW+K SFD+
Sbjct: 5 IHPVPAEWAREARYDAAGYEQLYGRSIADPGSFWLDQAKRLDWVKRPELAGDWSFDESDF 64
Query: 66 DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSE-SRNITYRELHEEVCKFANAL 124
I+WFADG LNV+ NC+DRHLA RGD++AIIWE DDP+E SR TYRELHEEVC+FAN L
Sbjct: 65 RIEWFADGKLNVAANCIDRHLASRGDEVAIIWEPDDPAEASRQFTYRELHEEVCRFANVL 124
Query: 125 RGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVI 184
+GQ V +GD VTIYMPMIPEA A+LAC R+GAIHSVVFGGFSPEALAGRI DC S VVI
Sbjct: 125 KGQGVKKGDRVTIYMPMIPEAAFAILACARLGAIHSVVFGGFSPEALAGRITDCDSSVVI 184
Query: 185 TADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVA 244
TADEG R GK+I LKANVD A +++KVIV K T G++ RD+WY +
Sbjct: 185 TADEGRRGGKRIALKANVDAAAER--APALEKVIVVKATGGHVTMTPGRDVWYHEAAAGV 242
Query: 245 GTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCT 304
GT C + M AE+ LFILYTSGSTGKPKGV HT+AGYLL+A+LTHE FDY+PG V+WC
Sbjct: 243 GTDCPAETMNAEDPLFILYTSGSTGKPKGVLHTSAGYLLWASLTHELAFDYRPGNVWWCA 302
Query: 305 ADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAM 364
AD+GWVTGHSYI+YGPLANGATTL++EG+PN+PD +R+ +V+D+H V ++TAPTA+RA+
Sbjct: 303 ADIGWVTGHSYILYGPLANGATTLMYEGLPNWPDASRIWQVVDRHNVHTIFTAPTALRAL 362
Query: 365 MASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLIS 424
M G V +SLRLLG+VGEPINPEAW WY++ VG+ RCPI+DTWWQTETGG +I+
Sbjct: 363 MKDGDDFVTKTSRTSLRLLGTVGEPINPEAWRWYHEVVGESRCPIIDTWWQTETGGAMIA 422
Query: 425 PLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRF 484
P+PGAT LKPGSATRP GV P LVD+ G ++ GA EGNLVI SWPGQ RT++GDH+RF
Sbjct: 423 PMPGATDLKPGSATRPLPGVDPQLVDSEGAVLHGATEGNLVIARSWPGQMRTVWGDHERF 482
Query: 485 VDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAE 544
TYF T+ G YFTGDG RRDEDGYYWITGRVDDV+NVSGHRMGTAE+ESA+V HPKVAE
Sbjct: 483 FQTYFTTYPGKYFTGDGCRRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVLHPKVAE 542
Query: 545 AAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPK 604
AAVVG+PHD+KGQGIY YVTLNAG +ALR EL WVR EIGPIA+PD +Q+APGLPK
Sbjct: 543 AAVVGMPHDVKGQGIYAYVTLNAGCAADDALRAELVKWVRTEIGPIATPDALQFAPGLPK 602
Query: 605 TRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
TRSGKIMRRILRKIA + LGD STLADP VV L+
Sbjct: 603 TRSGKIMRRILRKIAEGDVSSLGDTSTLADPSVVDDLV 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: 1489
Number of extensions: 68
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 Ga0059261_1313 Ga0059261_1313 (acetyl-coenzyme A synthetase (EC 6.2.1.1))
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.29392.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
5.3e-301 985.3 0.0 6.6e-301 985.0 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_1313 Ga0059261_1313 acetyl-coenzyme A
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1313 Ga0059261_1313 acetyl-coenzyme A synthetase (EC 6.2.1.1)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 985.0 0.0 6.6e-301 6.6e-301 5 627 .. 21 640 .. 18 642 .. 0.98
Alignments for each domain:
== domain 1 score: 985.0 bits; conditional E-value: 6.6e-301
TIGR02188 5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekr 70
y++ly ++i+dp +fw ++ak+ l+w+k e d+s+++ +++Wf+dg+lnv++nc+drh+++r
lcl|FitnessBrowser__Korea:Ga0059261_1313 21 AGYEQLYGRSIADPGSFWLDQAKR-LDWVKRPELAGDWSFDEsdfRIEWFADGKLNVAANCIDRHLASR 88
579********************5.**************99888899********************** PP
TIGR02188 71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGa 139
d+vaiiwe d++ e sr++tY+el++evcr+anvlk +Gvkkgdrv+iY+pmipea++a+lacaR+Ga
lcl|FitnessBrowser__Korea:Ga0059261_1313 89 GDEVAIIWEPDDPAEASRQFTYRELHEEVCRFANVLKGQGVKKGDRVTIYMPMIPEAAFAILACARLGA 157
********************************************************************* PP
TIGR02188 140 vhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeev 208
+hsvvf+Gfs+eala Ri+d+++ +vitadeg Rggk+i+lk++vd+a e+a+ ++ekv+vvk tg +v
lcl|FitnessBrowser__Korea:Ga0059261_1313 158 IHSVVFGGFSPEALAGRITDCDSSVVITADEGRRGGKRIALKANVDAAAERAP-ALEKVIVVKATGGHV 225
****************************************************9.7*************7 PP
TIGR02188 209 aewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfd 277
+ ++ grDvw++e+ + ++ ++c++e++++edplfiLYtsGstGkPkGvlht++Gyll+a+lt+++ fd
lcl|FitnessBrowser__Korea:Ga0059261_1313 226 T-MTPGRDVWYHEAAA-GVGTDCPAETMNAEDPLFILYTSGSTGKPKGVLHTSAGYLLWASLTHELAFD 292
6.**************.6*************************************************** PP
TIGR02188 278 ikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRa 346
+++++++wC+aD+GWvtGhsYi+ygPLanGattl++eg p++pdasr+w+v+++++v + +taPta+Ra
lcl|FitnessBrowser__Korea:Ga0059261_1313 293 YRPGNVWWCAADIGWVTGHSYILYGPLANGATTLMYEGLPNWPDASRIWQVVDRHNVHTIFTAPTALRA 361
********************************************************************* PP
TIGR02188 347 lmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvate 415
lmk g+++v+k+++ slr+lg+vGepinpeaw+Wy+evvG+++cpi+dtwWqtetGg++i+p+pg at+
lcl|FitnessBrowser__Korea:Ga0059261_1313 362 LMKDGDDFVTKTSRTSLRLLGTVGEPINPEAWRWYHEVVGESRCPIIDTWWQTETGGAMIAPMPG-ATD 429
*****************************************************************.6** PP
TIGR02188 416 lkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftG 484
lkpgsat+Pl+G+++++vd+eg ++ +e g Lvi ++wP+++rt++gd+erf++tYf++++g yftG
lcl|FitnessBrowser__Korea:Ga0059261_1313 430 LKPGSATRPLPGVDPQLVDSEGAVLHGATE-GNLVIARSWPGQMRTVWGDHERFFQTYFTTYPGKYFTG 497
*************************97777.79************************************ PP
TIGR02188 485 DgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkeg 553
Dg+rrd+dGy+wi+GRvDdvinvsGhr+gtae+esalv h++vaeaavvg+p+++kg+ i+a+v+l++g
lcl|FitnessBrowser__Korea:Ga0059261_1313 498 DGCRRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVLHPKVAEAAVVGMPHDVKGQGIYAYVTLNAG 566
********************************************************************* PP
TIGR02188 554 veedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledps 621
++d+ +l++el k+vr+eigpia+pd +++++ lPktRsGkimRR+lrkiaeg+ ++lgd+stl+dps
lcl|FitnessBrowser__Korea:Ga0059261_1313 567 CAADD-ALRAELVKWVRTEIGPIATPDALQFAPGLPKTRSGKIMRRILRKIAEGDvSSLGDTSTLADPS 634
**999.5************************************************************** PP
TIGR02188 622 vveelk 627
vv++l
lcl|FitnessBrowser__Korea:Ga0059261_1313 635 VVDDLV 640
**9986 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 12.26
//
[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