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)
>FitnessBrowser__Dyella79:N515DRAFT_3075
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.17104.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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 8.36
//
[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