Alignments for a candidate for acs in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Desulfovibrio vulgaris Miyazaki F

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate 8502070 DvMF_2783 acetate/CoA ligase (RefSeq)

Query= BRENDA::Q2XNL6
         (634 letters)



>FitnessBrowser__Miya:8502070
          Length = 651

 Score =  713 bits (1840), Expect = 0.0
 Identities = 347/641 (54%), Positives = 458/641 (71%), Gaps = 17/641 (2%)

Query: 8   LLEEKRVFKPHYTVVEEAHIKNWE---AELEKGKDHENYWAEKAERLEWFRKWDRVLDES 64
           LL E+RVF+P   VV  A +   +   A      D + YW E AE LEWFR+WD V D S
Sbjct: 11  LLREERVFRPLPQVVAGAVVNPQDVARARARAAADPDGYWEEAAEELEWFRRWDAVHDGS 70

Query: 65  NRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTAN 124
           N PF+RWF   + N+ +NA+DR ++T  +N++A+++  E GD R  TYY+LYREV+R AN
Sbjct: 71  NAPFHRWFTGARCNIVHNALDRHIETGTKNRLALIWEGESGDTRSFTYYQLYREVNRLAN 130

Query: 125 ALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKI 184
           AL+ LG+ KGD V +Y+P  PE V +MLA AKIGAVHS ++ G S  +L +R+ DAR  +
Sbjct: 131 ALRGLGVGKGDRVIIYMPPLPETVFAMLAAAKIGAVHSTVFGGFSARSLRDRMEDARPAV 190

Query: 185 IITADGTYRRGGVIKLKPIVDEAILQCPT-----IETTVVVKHTDIDIEMSDISGREMLF 239
           I+T DG YR G VI LKPI DEA+   P      +   VVV    ++  M++  GR++ +
Sbjct: 191 IVTVDGFYRNGRVIPLKPIADEAVATLPPDLAAGVRHMVVVHRAHVETPMTE--GRDIWY 248

Query: 240 DKLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHN 299
              + G+      E MD+ DPLF+LYTSG+TGKPKG +H  GGYMVGV  T+   FD+  
Sbjct: 249 HDAVRGQHHEALTEIMDSTDPLFLLYTSGTTGKPKGHVHAHGGYMVGVHRTMRWVFDVKP 308

Query: 300 GDLWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTA 359
            D++WCTA+ GWITGHSYVVYGPL+ GTTT+LYEG P YP+PG  WS+VE+ G+T  YTA
Sbjct: 309 TDIFWCTAEPGWITGHSYVVYGPLMAGTTTVLYEGHPLYPEPGRVWSMVERLGITILYTA 368

Query: 360 PTAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTE 419
           PT +R LMR G +H  R++L +L++LGTVGEPI+PEAW+W++R++GR +CP++DTWWQTE
Sbjct: 369 PTLVRMLMRHGAQHVARHDLTTLRLLGTVGEPISPEAWLWFHRHVGRGRCPVLDTWWQTE 428

Query: 420 TGMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLF 479
           TGM +++PLPV+ LKPGSVT+PLPGIEADVVDE+G PV  G GG LV+++PWPAM   ++
Sbjct: 429 TGMIMLSPLPVSLLKPGSVTRPLPGIEADVVDEHGKPVGPGHGGLLVLQRPWPAMSCGVY 488

Query: 480 NDEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFV 539
           ND++ Y  +YW++ PG  Y  GD+AR+DEDGYFWIQGR+DDVL IAGHRIGTAE+E+   
Sbjct: 489 NDDESYRRLYWERFPGW-YCTGDVARRDEDGYFWIQGRADDVLLIAGHRIGTAEMEAALA 547

Query: 540 AHPAVAEAAVIGKADPIKGEVIKAFLILKKGH-----KLNA-ALIEELKRHLRHELGPVA 593
           +H +VAE AVIG  D ++GEV KAF++L   H      +NA  L  EL  H+R ELGPVA
Sbjct: 548 SHRSVAECAVIGVPDALRGEVAKAFVVLVDDHPPLGTMVNADELAAELVEHVRRELGPVA 607

Query: 594 VVGEMVQVDSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634
           V+ E+   + LP+ RSGKIMRR+LR+ E G D GD STLE+
Sbjct: 608 VIREVSFREGLPRNRSGKIMRRVLRSEELGRDTGDLSTLED 648


Lambda     K      H
   0.319    0.138    0.428 

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: 1378
Number of extensions: 68
Number of successful extensions: 4
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: 634
Length of database: 651
Length adjustment: 38
Effective length of query: 596
Effective length of database: 613
Effective search space:   365348
Effective search space used:   365348
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 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate 8502070 DvMF_2783 (acetate/CoA ligase (RefSeq))
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.14176.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.3e-252  825.5   0.0   1.5e-252  825.3   0.0    1.0  1  lcl|FitnessBrowser__Miya:8502070  DvMF_2783 acetate/CoA ligase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8502070  DvMF_2783 acetate/CoA ligase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  825.3   0.0  1.5e-252  1.5e-252       5     620 ..      33     649 ..      29     651 .] 0.96

  Alignments for each domain:
  == domain 1  score: 825.3 bits;  conditional E-value: 1.5e-252
                         TIGR02188   5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiweg 80 
                                       ++ ++  ++a++dp+ +w++ a+ elew++ ++ v d s++p+ +Wf++++ n+  n++drh+e+ +k+++a+iweg
  lcl|FitnessBrowser__Miya:8502070  33 QDVARARARAAADPDGYWEEAAE-ELEWFRRWDAVHDGSNAPFHRWFTGARCNIVHNALDRHIETgTKNRLALIWEG 108
                                       56677788999********9998.6**************************************************** PP

                         TIGR02188  81 deegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRi 157
                                       + +g d+r++tY++l+rev+rlan+l+ lGv kgdrv+iY+p +pe+v+amla+a+iGavhs vf+Gfsa +l++R+
  lcl|FitnessBrowser__Miya:8502070 109 E-SG-DTRSFTYYQLYREVNRLANALRGLGVGKGDRVIIYMPPLPETVFAMLAAAKIGAVHSTVFGGFSARSLRDRM 183
                                       *.44.58********************************************************************** PP

                         TIGR02188 158 vdaeaklvitadeglRggkvielkkivdealekaee....svekvlvvkrtgeevaewkegrDvwweelvekeasae 230
                                       +da+  +++t d+ +R+g+vi+lk i+dea+++ +      v++++vv+r+  e ++++egrD+w++++v+ ++++e
  lcl|FitnessBrowser__Miya:8502070 184 EDARPAVIVTVDGFYRNGRVIPLKPIADEAVATLPPdlaaGVRHMVVVHRAHVE-TPMTEGRDIWYHDAVR-GQHHE 258
                                       ********************************987656668*************.66**************.699** PP

                         TIGR02188 231 cepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanG 307
                                         +e +ds dplf+LYtsG+tGkPkG +h+ gGy++ ++ t+++vfd+k++difwCta+ GW+tGhsY+vygPL++G
  lcl|FitnessBrowser__Miya:8502070 259 ALTEIMDSTDPLFLLYTSGTTGKPKGHVHAHGGYMVGVHRTMRWVFDVKPTDIFWCTAEPGWITGHSYVVYGPLMAG 335
                                       ***************************************************************************** PP

                         TIGR02188 308 attllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyev 384
                                        tt+l+eg p yp+++r+w+++e+ ++ti+YtaPt++R+lm+ g ++v++hdl +lr+lg+vGepi peaw W++++
  lcl|FitnessBrowser__Miya:8502070 336 TTTVLYEGHPLYPEPGRVWSMVERLGITILYTAPTLVRMLMRHGAQHVARHDLTTLRLLGTVGEPISPEAWLWFHRH 412
                                       ***************************************************************************** PP

                         TIGR02188 385 vGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrt 461
                                       vG+++cp+ dtwWqtetG i+++plp     lkpgs t+Pl+Giea+vvde+gk+v ++++ g+Lv+++pwP+m  +
  lcl|FitnessBrowser__Miya:8502070 413 VGRGRCPVLDTWWQTETGMIMLSPLPV--SLLKPGSVTRPLPGIEADVVDEHGKPVGPGHG-GLLVLQRPWPAMSCG 486
                                       **************************9..589**************************999.8************** PP

                         TIGR02188 462 iygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpde 538
                                       +y+d+e + + Y+++++g y tGD arrd+dGy+wi+GR+Ddv+ ++Ghr+gtae+e+al sh +vae+av+gvpd 
  lcl|FitnessBrowser__Miya:8502070 487 VYNDDESYRRLYWERFPGWYCTGDVARRDEDGYFWIQGRADDVLLIAGHRIGTAEMEAALASHRSVAECAVIGVPDA 563
                                       ***************************************************************************** PP

                         TIGR02188 539 ikgeaivafvvlkegve.....edeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeel 610
                                       ++ge+  afvvl + +       +++el++el ++vr+e+gp+a  +++ + e lP+ RsGkimRR+lr+   g++ 
  lcl|FitnessBrowser__Miya:8502070 564 LRGEVAKAFVVLVDDHPplgtmVNADELAAELVEHVRRELGPVAVIREVSFREGLPRNRSGKIMRRVLRSEELGRD- 639
                                       ************997762222245569******************************************9877765. PP

                         TIGR02188 611 lgdvstledp 620
                                       +gd+stled 
  lcl|FitnessBrowser__Miya:8502070 640 TGDLSTLEDG 649
                                       56******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (651 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 12.24
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources