Alignments for a candidate for acs in Dyadobacter tibetensis Y620-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Dyadobacter tibetensis Y620-1

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_025762291.1 X939_RS0105640 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000566685.1:WP_025762291.1
          Length = 629

 Score =  708 bits (1828), Expect = 0.0
 Identities = 350/625 (56%), Positives = 449/625 (71%), Gaps = 8/625 (1%)

Query: 22  QQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANC 81
           ++Y+  Y QS+  P+ FW E  +   W KP++KV N  F  G    KW+E G LN+  N 
Sbjct: 7   EEYQDTYNQSVEDPEGFWAEIAQQFTWRKPWKKVLNWDFTQGTT--KWFEGGELNITENA 64

Query: 82  LDRHLQENGDRTAIIWEGDDAS-QSKHISYKELHRDVCRFANTLLELGIKKGDVVAIYMP 140
           LDRHL + GD+ A+IWE +D   Q+ +I+YK LH  VCRFAN L + G+KKGD V IY+P
Sbjct: 65  LDRHLGDKGDQPALIWEPNDPDDQAVNITYKVLHDRVCRFANVLKKHGVKKGDRVCIYLP 124

Query: 141 MVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKK 200
           MVPE AVA+LACARIGA+HSV+FGGFS  ++A RI D+   +VITSD   R  + IP+K 
Sbjct: 125 MVPELAVAVLACARIGAIHSVVFGGFSARSIADRINDAQCVMVITSDGAFRGPKVIPMKD 184

Query: 201 NVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAEDPLF 260
            VDDAL+  +  SV+ V+V+ RT   +   +GRDLWW + V+       AE MNAEDPLF
Sbjct: 185 TVDDALEQCD--SVKKVIVMARTRTPVSMFKGRDLWWEEEVKHVDSNCPAEPMNAEDPLF 242

Query: 261 ILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGP 320
           ILYTSGSTGKPKGV+HT GGY++YA  TF  VF Y PG+I++CTAD+GW+TGHSY++YGP
Sbjct: 243 ILYTSGSTGKPKGVVHTCGGYMIYATYTFTNVFQYDPGEIHFCTADIGWITGHSYIVYGP 302

Query: 321 LACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSL 380
           L  GAT+++FEGVP +P  +R  ++V++H+VNILYTAPTAIR+LM  G   ++  D +SL
Sbjct: 303 LCAGATSVIFEGVPTFPDASRFWKIVERHKVNILYTAPTAIRSLMGYGLHFVKDHDLTSL 362

Query: 381 RILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSATRP 440
           + LGSVGEPIN EAW W+   IG   CP+VDTWWQTETGG MI+PL G T  K   AT P
Sbjct: 363 KKLGSVGEPINQEAWHWFKLNIGRNICPLVDTWWQTETGGIMISPLAGITPEKPSFATLP 422

Query: 441 FFGVQPALVDNEGNPLEG-ATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSG 499
             GVQP LVD +G+ LEG    G+L I   WPG  RT++GD ER +QTYFST+  MYF+G
Sbjct: 423 LPGVQPVLVDEKGDELEGNNVSGNLCIKFPWPGIIRTIYGDAERNKQTYFSTYPGMYFTG 482

Query: 500 DGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAI 559
           DG  RDEDG+Y ITGRVDDVLNVSGHR+GTAE+E+A+  H  + E+A+VG PH+IKGQ I
Sbjct: 483 DGCLRDEDGFYRITGRVDDVLNVSGHRIGTAEVENAINMHLGVVESAIVGYPHDIKGQGI 542

Query: 560 YAYVTLNHGEEPSPELYAE-VRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKI 618
           YA++  +   E  PE++ + +   V + IGP+A PD + +   LPKTRSGKIMRRILRKI
Sbjct: 543 YAFIITDQKPE-DPEMFRKGIAATVSRVIGPIAKPDKIQFVSGLPKTRSGKIMRRILRKI 601

Query: 619 AAGDTSNLGDTSTLADPGVVEKLLE 643
           + GD  +LGDTSTL DP +VE++ E
Sbjct: 602 SEGDFDSLGDTSTLLDPAIVEEIKE 626


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: 1345
Number of extensions: 65
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: 629
Length adjustment: 38
Effective length of query: 614
Effective length of database: 591
Effective search space:   362874
Effective search space used:   362874
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 WP_025762291.1 X939_RS0105640 (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.134506.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-289  947.5   0.0   1.7e-289  947.3   0.0    1.0  1  NCBI__GCF_000566685.1:WP_025762291.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000566685.1:WP_025762291.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  947.3   0.0  1.7e-289  1.7e-289       3     628 ..       5     626 ..       3     627 .. 0.98

  Alignments for each domain:
  == domain 1  score: 947.3 bits;  conditional E-value: 1.7e-289
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkv 74 
                                           + eey+++y++++edpe fwa+ a+ +++w kp++kvl++++++ ++kWfe+geln++ n++drh+ ++ d+ 
  NCBI__GCF_000566685.1:WP_025762291.1   5 TFEEYQDTYNQSVEDPEGFWAEIAQ-QFTWRKPWKKVLNWDFTQgTTKWFEGGELNITENALDRHLGDKGDQP 76 
                                           6799********************9.5****************99**************************** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           a+iwe +++++++ ++tY+ l+++vcr+anvlk++Gvkkgdrv+iYlpm+pe+++a+lacaRiGa+hsvvf+G
  NCBI__GCF_000566685.1:WP_025762291.1  77 ALIWEPNDPDDQAVNITYKVLHDRVCRFANVLKKHGVKKGDRVCIYLPMVPELAVAVLACARIGAIHSVVFGG 149
                                           ***********9************************************************************* PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
                                           fsa ++a+Ri+da++ +vit+d+++Rg kvi++k++vd+ale+++ sv+kv+v+ rt ++v+ + +grD+wwe
  NCBI__GCF_000566685.1:WP_025762291.1 150 FSARSIADRINDAQCVMVITSDGAFRGPKVIPMKDTVDDALEQCD-SVKKVIVMARTRTPVS-MFKGRDLWWE 220
                                           ********************************************8.7*************76.999******* PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           e+v++ ++++c++e++++edplfiLYtsGstGkPkGv+ht gGy+++a++t+  vf++ +++i++CtaD+GW+
  NCBI__GCF_000566685.1:WP_025762291.1 221 EEVKH-VDSNCPAEPMNAEDPLFILYTSGSTGKPKGVVHTCGGYMIYATYTFTNVFQYDPGEIHFCTADIGWI 292
                                           ****6.******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsYivygPL++Gat+++fegvpt+pdasrfw+++e++kv+i+YtaPtaiR+lm +g ++vk hdl sl+ l
  NCBI__GCF_000566685.1:WP_025762291.1 293 TGHSYIVYGPLCAGATSVIFEGVPTFPDASRFWKIVERHKVNILYTAPTAIRSLMGYGLHFVKDHDLTSLKKL 365
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           gsvGepin eaw+W++ ++G++ cp+vdtwWqtetGgi+i+pl+g +t+ kp+ atlPl+G+++++vde+g+e
  NCBI__GCF_000566685.1:WP_025762291.1 366 GSVGEPINQEAWHWFKLNIGRNICPLVDTWWQTETGGIMISPLAG-ITPEKPSFATLPLPGVQPVLVDEKGDE 437
                                           *********************************************.5************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           +e ++ +g L+ik pwP+++rtiygd er  +tYf++++g+yftGDg+ rd+dG++ i+GRvDdv+nvsGhr+
  NCBI__GCF_000566685.1:WP_025762291.1 438 LEGNNVSGNLCIKFPWPGIIRTIYGDAERNKQTYFSTYPGMYFTGDGCLRDEDGFYRITGRVDDVLNVSGHRI 510
                                           **666669***************************************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
                                           gtae+e+a+  h  v e+a+vg+p++ikg+ i+af++  ++ e  e  ++k + ++v++ igpiakpdki++v
  NCBI__GCF_000566685.1:WP_025762291.1 511 GTAEVENAINMHLGVVESAIVGYPHDIKGQGIYAFIITDQKPEDPE-MFRKGIAATVSRVIGPIAKPDKIQFV 582
                                           ************************************9998777555.7************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           + lPktRsGkimRR+lrki eg+ ++lgd+stl dp++vee+ke
  NCBI__GCF_000566685.1:WP_025762291.1 583 SGLPKTRSGKIMRRILRKISEGDfDSLGDTSTLLDPAIVEEIKE 626
                                           *****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (629 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: 23.93
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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