Alignments for a candidate for acs in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Desulfovibrio vulgaris Hildenborough

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 208482 DVU2969 acetoacetyl-CoA synthase

Query= SwissProt::P27550
         (652 letters)



>MicrobesOnline__882:208482
          Length = 661

 Score =  746 bits (1927), Expect = 0.0
 Identities = 367/623 (58%), Positives = 462/623 (74%), Gaps = 8/623 (1%)

Query: 25  EAMYQQSINVPDTFWGEQG-KILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANCLD 83
           EA+ +++   P+ FWGE+  +++DW KP+  V +         I+W++ G LN+A NCLD
Sbjct: 35  EALVRRAAEDPEGFWGERAAQLIDWFKPWDTVLDADM--NEPRIEWFKGGRLNVAHNCLD 92

Query: 84  RHLQENG-DRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAIYMPMV 142
           RH+  N  ++ AIIW+G+     + ++Y+ L+ +V RFA  L ++G+ KGD V++YMPM+
Sbjct: 93  RHVAGNRRNKAAIIWQGEPEEDVRVLTYQMLYDEVRRFAAVLRKMGVHKGDRVSLYMPMI 152

Query: 143 PEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKKNV 202
           PE AVAMLACARIGAVHS++F GFS  ++  RI D  +++V+T+D  +RAGR IPLK NV
Sbjct: 153 PELAVAMLACARIGAVHSIVFAGFSAVSLQNRIHDCEAKVVVTADAVLRAGRRIPLKVNV 212

Query: 203 DDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQAS--DQHQAEEMNAEDPLF 260
           D+A++     SVE VVV+ R   ++  +EGRDLWWH+++   +       EEM+AED LF
Sbjct: 213 DEAVRQ--CPSVEKVVVVNRGSLEVTMEEGRDLWWHEVMADRTLDVDRPCEEMDAEDMLF 270

Query: 261 ILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGP 320
           ILYTSGSTGKPKGV+HTTGGYL YAA T ++VFD    D+YWCTAD+GW+TGHSY++YGP
Sbjct: 271 ILYTSGSTGKPKGVVHTTGGYLTYAAHTTQWVFDVQDDDVYWCTADIGWITGHSYIVYGP 330

Query: 321 LACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSL 380
           LA GAT+LMFEGVP+WP+P R  ++V+K +VNI YTAPT +RALM EG    E  D SSL
Sbjct: 331 LALGATSLMFEGVPSWPSPDRFWRIVEKFRVNIFYTAPTVVRALMREGTDWTERHDLSSL 390

Query: 381 RILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSATRP 440
           R+LGSVGEPINPEAW WY   IG  + P+VDTWWQTETGG MI+ LP AT LK GSAT+P
Sbjct: 391 RVLGSVGEPINPEAWMWYHTHIGKGRLPIVDTWWQTETGGIMISGLPYATTLKPGSATQP 450

Query: 441 FFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSGD 500
             GV  A+V  +G+P      G LVI   WPG  R +FG  ER+  TYF  F  MY SGD
Sbjct: 451 LPGVDAAIVRPDGSPAGPNEGGHLVIRKPWPGMLRGIFGSPERYRSTYFERFPGMYESGD 510

Query: 501 GARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAIY 560
           GAR D DGY+WI GR+DDV+NVSGHR+GTAE+ESALVAHP +AEAAVVG+PH +KG+AIY
Sbjct: 511 GARTDTDGYFWIMGRLDDVINVSGHRMGTAEVESALVAHPSVAEAAVVGMPHAVKGEAIY 570

Query: 561 AYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAA 620
           AYVTL    E + EL AE+R WVRKEIGP+ATPDVL + + LPKTRSGKIMRRILRKIAA
Sbjct: 571 AYVTLGADAEETEELRAELRAWVRKEIGPIATPDVLQFAEGLPKTRSGKIMRRILRKIAA 630

Query: 621 GDTSNLGDTSTLADPGVVEKLLE 643
           G TS  GDTSTLADPGVV  L+E
Sbjct: 631 GATSEFGDTSTLADPGVVSDLIE 653


Lambda     K      H
   0.317    0.135    0.421 

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: 1389
Number of extensions: 64
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: 652
Length of database: 661
Length adjustment: 38
Effective length of query: 614
Effective length of database: 623
Effective search space:   382522
Effective search space used:   382522
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 208482 DVU2969 (acetoacetyl-CoA synthase)
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.3351.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     5e-302  988.7   0.0   5.8e-302  988.5   0.0    1.0  1  lcl|MicrobesOnline__882:208482  DVU2969 acetoacetyl-CoA synthase


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208482  DVU2969 acetoacetyl-CoA synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  988.5   0.0  5.8e-302  5.8e-302       5     628 ..      32     653 ..      28     654 .. 0.98

  Alignments for each domain:
  == domain 1  score: 988.5 bits;  conditional E-value: 5.8e-302
                       TIGR02188   5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvek.rkdkvaiiwegd 81 
                                      + ++l+++a+edpe fw++ a + ++w+kp+++vld+++++ +++Wf++g+lnv+ nc+drhv+  r++k+aiiw g+
  lcl|MicrobesOnline__882:208482  32 AAREALVRRAAEDPEGFWGERAAQLIDWFKPWDTVLDADMNEpRIEWFKGGRLNVAHNCLDRHVAGnRRNKAAIIWQGE 110
                                     5678899******************************998877*********************9889*********** PP

                       TIGR02188  82 eegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRivda 160
                                      ++ed+r ltY+ l++ev r+a+vl+++Gv+kgdrv++Y+pmipe+++amlacaRiGavhs+vfaGfsa +l++Ri+d+
  lcl|MicrobesOnline__882:208482 111 -PEEDVRVLTYQMLYDEVRRFAAVLRKMGVHKGDRVSLYMPMIPELAVAMLACARIGAVHSIVFAGFSAVSLQNRIHDC 188
                                     .6668************************************************************************** PP

                       TIGR02188 161 eaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvek.easaecepeklds 238
                                     eak+v+tad  lR g++i+lk +vdea+++++ svekv+vv+r   ev+ ++egrD+ww+e++++ + + + ++e++d+
  lcl|MicrobesOnline__882:208482 189 EAKVVVTADAVLRAGRRIPLKVNVDEAVRQCP-SVEKVVVVNRGSLEVT-MEEGRDLWWHEVMADrTLDVDRPCEEMDA 265
                                     *******************************9.7*************76.**************967788899****** PP

                       TIGR02188 239 edplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvp 317
                                     ed+lfiLYtsGstGkPkGv+httgGyl++aa t+++vfd++d+d++wCtaD+GW+tGhsYivygPLa Gat+l+fegvp
  lcl|MicrobesOnline__882:208482 266 EDMLFILYTSGSTGKPKGVVHTTGGYLTYAAHTTQWVFDVQDDDVYWCTADIGWITGHSYIVYGPLALGATSLMFEGVP 344
                                     ******************************************************************************* PP

                       TIGR02188 318 typdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtw 396
                                     ++p+++rfw+++ek++v+ifYtaPt++Ralm++g++++++hdlsslrvlgsvGepinpeaw+Wy++++Gk++ pivdtw
  lcl|MicrobesOnline__882:208482 345 SWPSPDRFWRIVEKFRVNIFYTAPTVVRALMREGTDWTERHDLSSLRVLGSVGEPINPEAWMWYHTHIGKGRLPIVDTW 423
                                     ******************************************************************************* PP

                       TIGR02188 397 WqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfk 475
                                     WqtetGgi+i+ lp  at lkpgsat+Pl+G++a++v  +g+++ ++e+ g Lvi+kpwP+mlr+i+g +er+ +tYf+
  lcl|MicrobesOnline__882:208482 424 WQTETGGIMISGLPY-ATTLKPGSATQPLPGVDAAIVRPDGSPAGPNEG-GHLVIRKPWPGMLRGIFGSPERYRSTYFE 500
                                     ***************.6*****************************999.8**************************** PP

                       TIGR02188 476 klkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegv 554
                                     +++g+y +GDgar+d+dGy+wi+GR+DdvinvsGhr+gtae+esalv+h++vaeaavvg+p+ +kgeai+a+v+l + +
  lcl|MicrobesOnline__882:208482 501 RFPGMYESGDGARTDTDGYFWIMGRLDDVINVSGHRMGTAEVESALVAHPSVAEAAVVGMPHAVKGEAIYAYVTLGADA 579
                                     ******************************************************************************9 PP

                       TIGR02188 555 eedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                     ee+e el++el+++vrkeigpia+pd ++++e lPktRsGkimRR+lrkia+g+ ++ gd+stl+dp vv +l+e
  lcl|MicrobesOnline__882:208482 580 EETE-ELRAELRAWVRKEIGPIATPDVLQFAEGLPKTRSGKIMRRILRKIAAGAtSEFGDTSTLADPGVVSDLIE 653
                                     9999.5***********************************************9999*************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (661 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: 12.87
//
[ok]

This GapMind analysis is from Sep 17 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:

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
the source code
instructions for running GapMind on your computer

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