GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Amycolatopsis xylanica CPCC 202699

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_091288310.1 BLV57_RS09725 acetate--CoA ligase

Query= SwissProt::P9WQD1
         (651 letters)



>NCBI__GCF_900107045.1:WP_091288310.1
          Length = 656

 Score =  883 bits (2281), Expect = 0.0
 Identities = 427/654 (65%), Positives = 511/654 (78%), Gaps = 16/654 (2%)

Query: 1   MSESTPEV------SSSYPPPAHFAEHANARAELYREAEEDRLAFWAKQANRLSWTTPFT 54
           M+E +P +      S ++PP  +F+  ANA+A+LY EA+ DR  FWA QA RLSW T ++
Sbjct: 1   MTEQSPALDNLLTESRTFPPNENFSAQANAKADLYAEADADREGFWAAQAERLSWDTKWS 60

Query: 55  EVLDWSGAPFAKWFVGGELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLA 114
           +VLDW+ APFAKWFVGG+LNVAYNCVDRHVE+GHGD++AIHW GEP GD R +TY++L  
Sbjct: 61  QVLDWTNAPFAKWFVGGKLNVAYNCVDRHVESGHGDQIAIHWVGEP-GDSRDITYAELKD 119

Query: 115 EVSKAANALTDLGLVAGDRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARI 174
           EVSKAAN L  +G+ AGDRVAI  P+IPEA++AMLACAR+G +HSVVFGGF+  AL++R+
Sbjct: 120 EVSKAANGLASIGVGAGDRVAIQCPMIPEAIVAMLACARIGALHSVVFGGFSPTALRSRV 179

Query: 175 VDAQAKLLITADGQFRRGKPSPLKAAADEALAAIPDCSVEHVLVVRRTGIEMAWSEGRDL 234
            D +AK++IT+DGQ+RRGK +P+K   DEAL      SVE VLV+RRTG E+   EGRDL
Sbjct: 180 DDQEAKVVITSDGQYRRGKAAPMKVNVDEALEGAE--SVEKVLVIRRTGDEIPLIEGRDL 237

Query: 235 WWHHVVGSASPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDV 294
           WWH +V   S  HTPE FDSEHPLF+LYTSGTTGKPKGI+HTSGGYLTQ  YT   +FD 
Sbjct: 238 WWHELVDGQSAEHTPEAFDSEHPLFILYTSGTTGKPKGILHTSGGYLTQAAYTHHNVFDH 297

Query: 295 KPDSDVFWCTADIGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIY 354
           K   DV+WCTADIGW+TGH+Y VYGPL N  T+V+YEGTP+TP   RH++II+KY V+IY
Sbjct: 298 KAGEDVYWCTADIGWITGHSYIVYGPLANRTTQVVYEGTPNTPHEGRHWEIIQKYKVSIY 357

Query: 355 YTAPTLIRMFMKWGREIPDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRTPLVDTWW 414
           YTAPTLIR FMKWG EIP  +D+SSLR+LGSVGEPINPEAW WYR+ IG G+ P+VDTWW
Sbjct: 358 YTAPTLIRTFMKWGNEIPQKYDISSLRVLGSVGEPINPEAWIWYRENIGAGQAPIVDTWW 417

Query: 415 QTETGSAMISPLPGIAAAKPGSAMTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQ 474
           QTETG  MISPLPG+ + KPGSA   LPGISAKIVDD  +      E  +   GYLVLD+
Sbjct: 418 QTETGGIMISPLPGVTSTKPGSAQRALPGISAKIVDDQAN------EVGKGGGGYLVLDK 471

Query: 475 PWPSMLRGIWGDPARYWHSYWSKFSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHR 534
           PWP MLRGIWGD AR+  +YWS+F+++GYYFAGDGA+ D DG IW+LGR+DDVMNVSGHR
Sbjct: 472 PWPGMLRGIWGDEARFKETYWSRFAEQGYYFAGDGAKYDADGDIWLLGRVDDVMNVSGHR 531

Query: 535 ISTAEVESALVAHSGVAEAAVVGVTDETTTQAICAFVVLRANYAP-HDRTAEELRTEVAR 593
           IST EVESALV+H  VAEAAVVG TD TT Q I AFV+LR N     D   +ELR  VA+
Sbjct: 532 ISTTEVESALVSHPTVAEAAVVGATDPTTGQGIVAFVILRGNAVDGGDAAVQELRNHVAK 591

Query: 594 VISPIARPRDVHVVPELPKTRSGKIMRRLLRDVAENRELGDTSTLLDPTVFDAI 647
            I PIA+PR + VV ELPKTRSGKIMRRLLRDVAENR +GD +TL D +V D I
Sbjct: 592 EIGPIAKPRQILVVQELPKTRSGKIMRRLLRDVAENRAVGDVTTLADSSVMDLI 645


Lambda     K      H
   0.319    0.136    0.433 

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: 1428
Number of extensions: 70
Number of successful extensions: 6
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: 656
Length adjustment: 38
Effective length of query: 613
Effective length of database: 618
Effective search space:   378834
Effective search space used:   378834
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate WP_091288310.1 BLV57_RS09725 (acetate--CoA ligase)
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.1907654.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-292  957.9   0.4   1.2e-292  957.7   0.4    1.0  1  NCBI__GCF_900107045.1:WP_091288310.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900107045.1:WP_091288310.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  957.7   0.4  1.2e-292  1.2e-292       3     627 ..      27     646 ..      25     648 .. 0.98

  Alignments for each domain:
  == domain 1  score: 957.7 bits;  conditional E-value: 1.2e-292
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkv 74 
                                           ++++ ++ly+ea +d+e fwa +a+ +l+w++++++vld++++p++kWf++g+lnv+yncvdrhve+ + d++
  NCBI__GCF_900107045.1:WP_091288310.1  27 QANAKADLYAEADADREGFWAAQAE-RLSWDTKWSQVLDWTNAPFAKWFVGGKLNVAYNCVDRHVESgHGDQI 98 
                                           5678899*****************9.5********************************************** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           ai+w g+ +g dsr +tYael++ev+++an l ++Gv  gdrvai  pmipea++amlacaRiGa+hsvvf+G
  NCBI__GCF_900107045.1:WP_091288310.1  99 AIHWVGE-PG-DSRDITYAELKDEVSKAANGLASIGVGAGDRVAIQCPMIPEAIVAMLACARIGALHSVVFGG 169
                                           ******9.77.59************************************************************ PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
                                           fs+ al++R+ d eak+vit+d+++R+gk+ ++k +vdeale ae svekvlv++rtg+e+  + egrD+ww+
  NCBI__GCF_900107045.1:WP_091288310.1 170 FSPTALRSRVDDQEAKVVITSDGQYRRGKAAPMKVNVDEALEGAE-SVEKVLVIRRTGDEIP-LIEGRDLWWH 240
                                           ******************************************998.8*************66.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik.dedifwCtaDvGW 292
                                           elv+ ++sae++pe++dse+plfiLYtsG+tGkPkG+lht+gGyl++aa+t++ vfd+k  ed++wCtaD+GW
  NCBI__GCF_900107045.1:WP_091288310.1 241 ELVD-GQSAEHTPEAFDSEHPLFILYTSGTTGKPKGILHTSGGYLTQAAYTHHNVFDHKaGEDVYWCTADIGW 312
                                           ****.6*****************************************************668*********** PP

                             TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365
                                           +tGhsYivygPLan  t++++eg+p++p+++r+we+i+kykv+i+YtaPt+iR++mk+g+e+++k+d+sslrv
  NCBI__GCF_900107045.1:WP_091288310.1 313 ITGHSYIVYGPLANRTTQVVYEGTPNTPHEGRHWEIIQKYKVSIYYTAPTLIRTFMKWGNEIPQKYDISSLRV 385
                                           ************************************************************************* PP

                             TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438
                                           lgsvGepinpeaw Wy+e++G +++pivdtwWqtetGgi+i+plpg +t++kpgsa++ l+Gi+a++vd++++
  NCBI__GCF_900107045.1:WP_091288310.1 386 LGSVGEPINPEAWIWYRENIGAGQAPIVDTWWQTETGGIMISPLPG-VTSTKPGSAQRALPGISAKIVDDQAN 457
                                           **********************************************.5************************* PP

                             TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkdGyiwilGRvDdvinvsG 509
                                           ev ++ + g+Lv++kpwP+mlr+i+gde rf etY++++ +  +yf+GDga+ d+dG+iw+lGRvDdv+nvsG
  NCBI__GCF_900107045.1:WP_091288310.1 458 EVGKGGG-GYLVLDKPWPGMLRGIWGDEARFKETYWSRFAEqgYYFAGDGAKYDADGDIWLLGRVDDVMNVSG 529
                                           ***9988.8*****************************98777****************************** PP

                             TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdki 582
                                           hr++t+e+esalvsh++vaeaavvg++d ++g+ ivafv+l+ ++    ++  +el+++v+keigpiakp++i
  NCBI__GCF_900107045.1:WP_091288310.1 530 HRISTTEVESALVSHPTVAEAAVVGATDPTTGQGIVAFVILRGNAVDGGDAAVQELRNHVAKEIGPIAKPRQI 602
                                           *******************************************99998889********************** PP

                             TIGR02188 583 lvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                           lvv+elPktRsGkimRRllr++ae++  +gdv+tl+d+sv++ ++
  NCBI__GCF_900107045.1:WP_091288310.1 603 LVVQELPKTRSGKIMRRLLRDVAENRA-VGDVTTLADSSVMDLIS 646
                                           ***********************9765.67**********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (656 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 21.18
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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