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.27417.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.85
//
[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:
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