Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate N515DRAFT_3075 N515DRAFT_3075 acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= reanno::pseudo5_N2C3_1:AO356_18695
(651 letters)
>lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 N515DRAFT_3075
acetyl-coenzyme A synthetase (EC 6.2.1.1)
Length = 646
Score = 909 bits (2350), Expect = 0.0
Identities = 432/640 (67%), Positives = 514/640 (80%)
Query: 4 ASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDH 63
+ +YPV+PE AA + Y+ +Y++SV +P+GFW +RL+W + + +K S+D
Sbjct: 2 SKVYPVKPEFAAKARISKEDYERLYEESVRDPEGFWGRIGERLEWHRKPSKIKNVSYDPK 61
Query: 64 HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
++ I+W+ DG LNVS NCLDRHLA RGD+ AII+EGDDP+ESR++TYRELH EVCKFAN
Sbjct: 62 NLHIRWYEDGELNVSANCLDRHLASRGDKTAIIFEGDDPNESRHLTYRELHAEVCKFANT 121
Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
L+ V +GD V IYMPMIPEA VAMLAC RIGA+HSVVFGGFSP++LAGRI D +KVV
Sbjct: 122 LKNLGVAKGDRVAIYMPMIPEAAVAMLACARIGAVHSVVFGGFSPDSLAGRIADSTAKVV 181
Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
+TADEGVR GKKIPLKANVD AL P T+S++ VIV +RT + RD +Y LM+
Sbjct: 182 VTADEGVRGGKKIPLKANVDAALERPGTNSVETVIVVRRTGSAVPMQSPRDRYYHVLMEG 241
Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
C P + AE LFILYTSGSTGKPKGV HT+ GYL++A THE VFD + +VYWC
Sbjct: 242 QSADCPPTPVEAEHPLFILYTSGSTGKPKGVLHTSGGYLVFAGFTHEMVFDLREDDVYWC 301
Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
TADVGWVTGHSY+VYGPLANGATT++F+GVPNYPD +R V+DKHKV++ YTAPTAIRA
Sbjct: 302 TADVGWVTGHSYVVYGPLANGATTVMFDGVPNYPDTSRFWNVVDKHKVTLFYTAPTAIRA 361
Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
+M G A V+ A +SLRLLGSVGEPINPEAW+WYY+ VG ERCPIVDTWWQTETGG++I
Sbjct: 362 LMREGEAPVKKASRASLRLLGSVGEPINPEAWEWYYRVVGDERCPIVDTWWQTETGGIMI 421
Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
+PL GA KPGSAT+PFFG+ PA+VD G ++EGA EGNLVI DSWPGQ RT+YGDH R
Sbjct: 422 TPLAGAIDAKPGSATKPFFGIRPAVVDAGGAVLEGATEGNLVIADSWPGQMRTVYGDHQR 481
Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
FV+TYF + G YFTGDG RRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+V+HPKVA
Sbjct: 482 FVETYFTAYPGNYFTGDGVRRDEDGYYWITGRVDDVINVSGHRIGTAEVESALVSHPKVA 541
Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
EAAVVG PH+IKGQGIY YVTL AGE+ S+ LR EL WVRKEIGPIA+PD +QWAPGLP
Sbjct: 542 EAAVVGCPHEIKGQGIYAYVTLIAGEQGSDELRKELVAWVRKEIGPIATPDYLQWAPGLP 601
Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
KTRSGKIMRRILRKI + D LGDISTLADP VV +L+E
Sbjct: 602 KTRSGKIMRRILRKIGENQPDQLGDISTLADPSVVKNLVE 641
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: 1422
Number of extensions: 75
Number of successful extensions: 1
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: 646
Length adjustment: 38
Effective length of query: 613
Effective length of database: 608
Effective search space: 372704
Effective search space used: 372704
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 N515DRAFT_3075 N515DRAFT_3075 (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.13910.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 1024.9 0.0 0 1024.7 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 N515DRAFT_3075 acetyl-coenzyme A
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 N515DRAFT_3075 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 ! 1024.7 0.0 0 0 3 628 .. 18 641 .. 16 642 .. 0.98
Alignments for each domain:
== domain 1 score: 1024.7 bits; conditional E-value: 0
TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdr 65
+ e+y++lyee+++dpe fw++ ++ +lew+++ +k+++ s +p +++W+edgelnvs+nc+dr
lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 18 SKEDYERLYEESVRDPEGFWGRIGE-RLEWHRKPSKIKNVSYDPknlHIRWYEDGELNVSANCLDR 82
5789********************9.5************9998877899***************** PP
TIGR02188 66 hvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviam 131
h+++r dk+aii+egd+++e sr+ltY+el++evc++an+lk+lGv kgdrvaiY+pmipea++am
lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 83 HLASRGDKTAIIFEGDDPNE-SRHLTYRELHAEVCKFANTLKNLGVAKGDRVAIYMPMIPEAAVAM 147
******************96.********************************************* PP
TIGR02188 132 lacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.sve 196
lacaRiGavhsvvf+Gfs+++la Ri d++ak+v+tadeg+Rggk+i+lk++vd+ale+ + sve
lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 148 LACARIGAVHSVVFGGFSPDSLAGRIADSTAKVVVTADEGVRGGKKIPLKANVDAALERPGTnSVE 213
***********************************************************9988*** PP
TIGR02188 197 kvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttg 262
+v+vv+rtg+ v +++ rD +++ l+e ++sa+c+p+++++e+plfiLYtsGstGkPkGvlht+g
lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 214 TVIVVRRTGSAVP-MQSPRDRYYHVLME-GQSADCPPTPVEAEHPLFILYTSGSTGKPKGVLHTSG 277
***********66.**************.6************************************ PP
TIGR02188 263 GylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfwev 328
Gyl+ a t+++vfd++++d++wCtaDvGWvtGhsY+vygPLanGatt++f+gvp+ypd+srfw+v
lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 278 GYLVFAGFTHEMVFDLREDDVYWCTADVGWVTGHSYVVYGPLANGATTVMFDGVPNYPDTSRFWNV 343
****************************************************************** PP
TIGR02188 329 iekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivd 394
++k+kvt fYtaPtaiRalm++ge+ vkk ++ slr+lgsvGepinpeaweWyy+vvG+e+cpivd
lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 344 VDKHKVTLFYTAPTAIRALMREGEAPVKKASRASLRLLGSVGEPINPEAWEWYYRVVGDERCPIVD 409
****************************************************************** PP
TIGR02188 395 twWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlr 460
twWqtetGgi+itpl+g a+++kpgsat+P+fGi+++vvd g +e +e g Lvi ++wP+++r
lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 410 TWWQTETGGIMITPLAG-AIDAKPGSATKPFFGIRPAVVDAGGAVLEGATE-GNLVIADSWPGQMR 473
*****************.6***************************97777.79************ PP
TIGR02188 461 tiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvshea 526
t+ygd++rfvetYf++++g yftGDg+rrd+dGy+wi+GRvDdvinvsGhr+gtae+esalvsh++
lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 474 TVYGDHQRFVETYFTAYPGNYFTGDGVRRDEDGYYWITGRVDDVINVSGHRIGTAEVESALVSHPK 539
****************************************************************** PP
TIGR02188 527 vaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktR 592
vaeaavvg p+eikg+ i+a+v+l +g++ ++ el+kel ++vrkeigpia+pd +++++ lPktR
lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 540 VAEAAVVGCPHEIKGQGIYAYVTLIAGEQGSD-ELRKELVAWVRKEIGPIATPDYLQWAPGLPKTR 604
*****************************999.5******************************** PP
TIGR02188 593 sGkimRRllrkiaege.ellgdvstledpsvveelke 628
sGkimRR+lrki e++ ++lgd+stl+dpsvv++l e
lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 605 SGKIMRRILRKIGENQpDQLGDISTLADPSVVKNLVE 641
*********************************9976 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (646 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: 00:00:00.04
# Mc/sec: 8.84
//
[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