GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Rhodococcus qingshengii djl-6-2

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_050655293.1 C1M55_RS02775 acetate--CoA ligase

Query= SwissProt::P9WQD1
         (651 letters)



>NCBI__GCF_002893965.1:WP_050655293.1
          Length = 643

 Score =  941 bits (2433), Expect = 0.0
 Identities = 453/648 (69%), Positives = 530/648 (81%), Gaps = 10/648 (1%)

Query: 2   SESTPEVSSSYPPPAHFAEHANARAELYREAEEDRLAFWAKQANRLSWTTPFTEVLDWSG 61
           S +  +V  +YPP A FA  ANA  EL   A+ DRLAFWA QA RL W   +T+VLDW+ 
Sbjct: 3   SAAETDVPQAYPPSAEFAAAANAGPELQAAADTDRLAFWANQAERLHWHEKWTDVLDWTD 62

Query: 62  APFAKWFVGGELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLAEVSKAAN 121
           AP AKWFVGG+LNVAYNCVDRHV AG+GDR+AIH+EGEP GD R LTY+DLLAEVS+AAN
Sbjct: 63  APVAKWFVGGKLNVAYNCVDRHVLAGNGDRIAIHFEGEP-GDSRDLTYNDLLAEVSRAAN 121

Query: 122 ALTDLGLVAGDRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARIVDAQAKL 181
             TDLGLVAGDRVAIY+P+IPEA++ MLACARLG+ HSVVF GF+A AL++RI DAQAKL
Sbjct: 122 TFTDLGLVAGDRVAIYMPMIPEAIVTMLACARLGLTHSVVFAGFSATALRSRIDDAQAKL 181

Query: 182 LITADGQFRRGKPSPLKAAADEALAAIPDCSVEHVLVVRRTGIEMAWSEGRDLWWHHVVG 241
           ++T DGQ+RRG  +P+K A DE++A     SV++VLVV RTGI++ W++GRDLWWH  V 
Sbjct: 182 VVTVDGQWRRGAAAPIKTAVDESVAGAE--SVQNVLVVNRTGIDVDWTDGRDLWWHETVA 239

Query: 242 SASPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDVKPDSDVF 301
            ASP H  + FD+EHPLF+LYTSGTTGKPKGI+HTSGGYLTQ  YT   +FD K   DV+
Sbjct: 240 QASPEHEAQAFDAEHPLFILYTSGTTGKPKGIIHTSGGYLTQASYTHHNVFDHKAGQDVY 299

Query: 302 WCTADIGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIYYTAPTLI 361
           WCTADIGWVTGH+Y VYGPL NGVT+V+YEGTP++P+ HRHF IIEKYGV+IYYTAPTL+
Sbjct: 300 WCTADIGWVTGHSYIVYGPLSNGVTQVVYEGTPNSPNEHRHFDIIEKYGVSIYYTAPTLV 359

Query: 362 RMFMKWGREIPDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRTPLVDTWWQTETGSA 421
           R FMKWGREIPD+HDLSS+RLLGSVGEPINPEAWRW+R+VIGG + P+VDTWWQTETG+ 
Sbjct: 360 RTFMKWGREIPDAHDLSSIRLLGSVGEPINPEAWRWFREVIGGNKAPIVDTWWQTETGAI 419

Query: 422 MISPLPGIAAAKPGSAMTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQPWPSMLR 481
           MISPLPGI A KPGSAM PLPGISAKIVDD   PL P         GYLVLD+PWP+MLR
Sbjct: 420 MISPLPGITATKPGSAMAPLPGISAKIVDDDAKPLGPGG------NGYLVLDEPWPAMLR 473

Query: 482 GIWGDPARYWHSYWSKFSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHRISTAEVE 541
           GIWGD  RY  +YWS+++++G+YFAGDGA+ D DGA+WVLGR+DDVMNVSGHRIST+EVE
Sbjct: 474 GIWGDMDRYRDTYWSRYAEEGWYFAGDGAKYDDDGALWVLGRVDDVMNVSGHRISTSEVE 533

Query: 542 SALVAHSGVAEAAVVGVTDETTTQAICAFVVLRANYA-PHDRTAEELRTEVARVISPIAR 600
           SALV H GVAEAAVVG  DETT Q I AFV+LR       D    EL+ +V+  ISPIA+
Sbjct: 534 SALVNHHGVAEAAVVGAADETTGQGIVAFVILREGVENTGDVLIAELKAQVSTDISPIAK 593

Query: 601 PRDVHVVPELPKTRSGKIMRRLLRDVAENRELGDTSTLLDPTVFDAIR 648
           PR + +VPELPKTRSGKIMRRLLRDVAE R+LGDTSTL+DP VFDAIR
Sbjct: 594 PRQITIVPELPKTRSGKIMRRLLRDVAEGRDLGDTSTLVDPKVFDAIR 641


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: 1524
Number of extensions: 89
Number of successful extensions: 5
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: 643
Length adjustment: 38
Effective length of query: 613
Effective length of database: 605
Effective search space:   370865
Effective search space used:   370865
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_050655293.1 C1M55_RS02775 (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.1371197.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-287  939.9   0.2   3.4e-287  939.7   0.2    1.0  1  NCBI__GCF_002893965.1:WP_050655293.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_050655293.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  939.7   0.2  3.4e-287  3.4e-287       8     627 ..      27     641 ..      20     643 .] 0.98

  Alignments for each domain:
  == domain 1  score: 939.7 bits;  conditional E-value: 3.4e-287
                             TIGR02188   8 kelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiwe 79 
                                            el + a +d+ +fwa++a+ +l+w+++++ vld++ +p +kWf++g+lnv+yncvdrhv + + d++ai++e
  NCBI__GCF_002893965.1:WP_050655293.1  27 PELQAAADTDRLAFWANQAE-RLHWHEKWTDVLDWTDAPVAKWFVGGKLNVAYNCVDRHVLAgNGDRIAIHFE 98 
                                           5778889999*********9.5**************************************999********** PP

                             TIGR02188  80 gdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaea 152
                                           g+ +g dsr ltY++ll+ev+r+an++++lG+  gdrvaiY+pmipea+++mlacaR+G +hsvvfaGfsa a
  NCBI__GCF_002893965.1:WP_050655293.1  99 GE-PG-DSRDLTYNDLLAEVSRAANTFTDLGLVAGDRVAIYMPMIPEAIVTMLACARLGLTHSVVFAGFSATA 169
                                           **.77.59***************************************************************** PP

                             TIGR02188 153 laeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvek 225
                                           l++Ri da+aklv+t d+++R+g + ++k++vde+++ ae sv++vlvv+rtg +v  w++grD+ww+e+v++
  NCBI__GCF_002893965.1:WP_050655293.1 170 LRSRIDDAQAKLVVTVDGQWRRGAAAPIKTAVDESVAGAE-SVQNVLVVNRTGIDVD-WTDGRDLWWHETVAQ 240
                                           *************************************998.8*************66.**************6 PP

                             TIGR02188 226 easaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik.dedifwCtaDvGWvtGhs 297
                                            as e+e++++d+e+plfiLYtsG+tGkPkG++ht+gGyl++a++t++ vfd+k  +d++wCtaD+GWvtGhs
  NCBI__GCF_002893965.1:WP_050655293.1 241 -ASPEHEAQAFDAEHPLFILYTSGTTGKPKGIIHTSGGYLTQASYTHHNVFDHKaGQDVYWCTADIGWVTGHS 312
                                           .*****************************************************668**************** PP

                             TIGR02188 298 YivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvG 370
                                           YivygPL+nG+t++++eg+p+ p+++r++++ieky+v+i+YtaPt++R++mk+g+e++++hdlss+r+lgsvG
  NCBI__GCF_002893965.1:WP_050655293.1 313 YIVYGPLSNGVTQVVYEGTPNSPNEHRHFDIIEKYGVSIYYTAPTLVRTFMKWGREIPDAHDLSSIRLLGSVG 385
                                           ************************************************************************* PP

                             TIGR02188 371 epinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveee 443
                                           epinpeaw+W++ev+G +k+pivdtwWqtetG+i+i+plpg +t++kpgsa+ Pl+Gi+a++vd+++k++ ++
  NCBI__GCF_002893965.1:WP_050655293.1 386 EPINPEAWRWFREVIGGNKAPIVDTWWQTETGAIMISPLPG-ITATKPGSAMAPLPGISAKIVDDDAKPLGPG 457
                                           *****************************************.5****************************99 PP

                             TIGR02188 444 eeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkdGyiwilGRvDdvinvsGhrlgt 514
                                            + g+Lv+++pwP+mlr+i+gd +r+ +tY++++ +   yf+GDga+ d+dG +w+lGRvDdv+nvsGhr++t
  NCBI__GCF_002893965.1:WP_050655293.1 458 GN-GYLVLDEPWPAMLRGIWGDMDRYRDTYWSRYAEegWYFAGDGAKYDDDGALWVLGRVDDVMNVSGHRIST 529
                                           88.8*****************************987779********************************** PP

                             TIGR02188 515 aeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvvee 587
                                           +e+esalv+h+ vaeaavvg++de++g+ ivafv+l+egve++ + l +elk++v++ i+piakp++i++v+e
  NCBI__GCF_002893965.1:WP_050655293.1 530 SEVESALVNHHGVAEAAVVGAADETTGQGIVAFVILREGVENTGDVLIAELKAQVSTDISPIAKPRQITIVPE 602
                                           *******************************************99**************************** PP

                             TIGR02188 588 lPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                           lPktRsGkimRRllr++aeg++l gd+stl dp+v+++++
  NCBI__GCF_002893965.1:WP_050655293.1 603 LPKTRSGKIMRRLLRDVAEGRDL-GDTSTLVDPKVFDAIR 641
                                           *******************9875.6***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (643 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 24.78
//
[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