Alignments for a candidate for acs in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Caulobacter crescentus NA1000

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate CCNA_03696 CCNA_03696 acetyl-coenzyme A synthetase

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>FitnessBrowser__Caulo:CCNA_03696
          Length = 647

 Score =  852 bits (2202), Expect = 0.0
 Identities = 411/643 (63%), Positives = 493/643 (76%), Gaps = 2/643 (0%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           +S   ++PV  ++A     D A Y A   +   +P+G+WR+ A RLDWI P T +K  S+
Sbjct: 2   VSDGQVFPVPADLARDAHIDAAAYDAALARVEADPEGYWRDIAARLDWITPPTKIKDVSY 61

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
                 I+W+ DG LNVS NC+DRHL  + D +A+++EGD+P  S  +TY +LHEEVC+ 
Sbjct: 62  AKEDFRIRWYEDGVLNVSANCIDRHLPAKKDDVALVFEGDEPGTSSTLTYGQLHEEVCRM 121

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           AN L+ Q V +GD VTIY+PM+P A VAMLAC RIGA+HSVVFGGFSP+++AGRI DC S
Sbjct: 122 ANVLKAQGVKKGDRVTIYLPMVPLAAVAMLACARIGAVHSVVFGGFSPDSIAGRIQDCAS 181

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
             VITADEG R G+++PLKAN+D+AL +     + KV++ + T  ++     RDI ++D+
Sbjct: 182 HFVITADEGRRGGRRVPLKANIDEALKH--CPWVGKVLMIRWTGADVPLKAGRDIVWQDV 239

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
                  C P+ M AE+ LFILYTSGSTGKPKGV HTT GYL +A+ T   VFDYKPGEV
Sbjct: 240 RDTVSADCPPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLAWASWTFWAVFDYKPGEV 299

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           +WCTADVGWVTGHSY+VYGPLANG T+L+FEGVPNYP  +R  +VIDKH+VSI YTAPTA
Sbjct: 300 FWCTADVGWVTGHSYVVYGPLANGGTSLIFEGVPNYPTPSRFWEVIDKHQVSIFYTAPTA 359

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           +RA+M  G A V   D SSLRLLGSVGEPINPEAW WY++ VGKE+ PIVDTWWQTETGG
Sbjct: 360 LRALMREGDAHVTKNDLSSLRLLGSVGEPINPEAWLWYHRVVGKEKLPIVDTWWQTETGG 419

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LI+PLPGATALKPGSA++P  GV P LVD  G  ++GA EGNLVI DSWPGQ RT+YGD
Sbjct: 420 MLITPLPGATALKPGSASKPLPGVKPQLVDAEGKFLDGATEGNLVITDSWPGQMRTVYGD 479

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           H RF +TYF T+ G YFTGDG RRD DGYYWITGRVDDV+NVSGHR+GTAEIESA+VAH 
Sbjct: 480 HQRFFETYFSTYPGKYFTGDGCRRDADGYYWITGRVDDVINVSGHRLGTAEIESALVAHE 539

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
            VAEAAVVG PHDIKGQG+Y YVTL AG E ++ALR +L  WVR EIGP A+PDVIQWAP
Sbjct: 540 TVAEAAVVGYPHDIKGQGVYAYVTLKAGIEATDALRKDLVLWVRHEIGPFAAPDVIQWAP 599

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           GLPKTRSGKIMRRILRKIA  E   LGD STLADP VV  L++
Sbjct: 600 GLPKTRSGKIMRRILRKIAENELGSLGDTSTLADPSVVDDLVK 642


Lambda     K      H
   0.318    0.135    0.418 

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: 1483
Number of extensions: 66
Number of successful extensions: 2
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: 647
Length adjustment: 38
Effective length of query: 613
Effective length of database: 609
Effective search space:   373317
Effective search space used:   373317
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 CCNA_03696 CCNA_03696 (acetyl-coenzyme A synthetase)
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.18516.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-302  990.7   0.0   1.5e-302  990.5   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03696  CCNA_03696 acetyl-coenzyme A syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03696  CCNA_03696 acetyl-coenzyme A synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  990.5   0.0  1.5e-302  1.5e-302       4     628 ..      22     642 ..      19     643 .. 0.98

  Alignments for each domain:
  == domain 1  score: 990.5 bits;  conditional E-value: 1.5e-302
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           + +y +  ++ ++dpe +w++ a  +l+w++p +k++d s ++   +++W+edg lnvs+nc+drh+ ++kd 
  lcl|FitnessBrowser__Caulo:CCNA_03696  22 AAAYDAALARVEADPEGYWRDIAA-RLDWITPPTKIKDVSYAKedfRIRWYEDGVLNVSANCIDRHLPAKKDD 93 
                                           56899999999************9.5************998877789************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           va+++egde+g+ s +ltY +l++evcr+anvlk++Gvkkgdrv+iYlpm+p a++amlacaRiGavhsvvf+
  lcl|FitnessBrowser__Caulo:CCNA_03696  94 VALVFEGDEPGT-SSTLTYGQLHEEVCRMANVLKAQGVKKGDRVTIYLPMVPLAAVAMLACARIGAVHSVVFG 165
                                           ***********7.************************************************************ PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219
                                           Gfs++++a Ri+d+ +++vitadeg Rgg++++lk+++deal++++  v kvl+++ tg++v  +k grD++w
  lcl|FitnessBrowser__Caulo:CCNA_03696 166 GFSPDSIAGRIQDCASHFVITADEGRRGGRRVPLKANIDEALKHCP-WVGKVLMIRWTGADVP-LKAGRDIVW 236
                                           *********************************************9.7*************66.********* PP

                             TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292
                                           +++ ++ +sa+c+pe++++edplfiLYtsGstGkPkGvlhttgGyl +a+ t+  vfd+k++++fwCtaDvGW
  lcl|FitnessBrowser__Caulo:CCNA_03696 237 QDVRDT-VSADCPPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLAWASWTFWAVFDYKPGEVFWCTADVGW 308
                                           ***995.****************************************************************** PP

                             TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365
                                           vtGhsY+vygPLanG t+l+fegvp+yp++srfwevi+k++v+ifYtaPta+Ralm++g+++v+k dlsslr+
  lcl|FitnessBrowser__Caulo:CCNA_03696 309 VTGHSYVVYGPLANGGTSLIFEGVPNYPTPSRFWEVIDKHQVSIFYTAPTALRALMREGDAHVTKNDLSSLRL 381
                                           ************************************************************************* PP

                             TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438
                                           lgsvGepinpeaw Wy++vvGkek pivdtwWqtetGg+litplpg at+lkpgsa++Pl+G+++++vd egk
  lcl|FitnessBrowser__Caulo:CCNA_03696 382 LGSVGEPINPEAWLWYHRVVGKEKLPIVDTWWQTETGGMLITPLPG-ATALKPGSASKPLPGVKPQLVDAEGK 453
                                           **********************************************.6************************* PP

                             TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhr 511
                                            ++  +e g Lvi+++wP+++rt+ygd++rf+etYf++++g yftGDg+rrd+dGy+wi+GRvDdvinvsGhr
  lcl|FitnessBrowser__Caulo:CCNA_03696 454 FLDGATE-GNLVITDSWPGQMRTVYGDHQRFFETYFSTYPGKYFTGDGCRRDADGYYWITGRVDDVINVSGHR 525
                                           ***8777.79*************************************************************** PP

                             TIGR02188 512 lgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilv 584
                                           lgtaeiesalv+he+vaeaavvg+p++ikg+ ++a+v+lk+g+e+++ +l+k+l  +vr+eigp+a+pd i++
  lcl|FitnessBrowser__Caulo:CCNA_03696 526 LGTAEIESALVAHETVAEAAVVGYPHDIKGQGVYAYVTLKAGIEATD-ALRKDLVLWVRHEIGPFAAPDVIQW 597
                                           ********************************************999.5************************ PP

                             TIGR02188 585 veelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           ++ lPktRsGkimRR+lrkiae+e  +lgd+stl+dpsvv++l +
  lcl|FitnessBrowser__Caulo:CCNA_03696 598 APGLPKTRSGKIMRRILRKIAENElGSLGDTSTLADPSVVDDLVK 642
                                           *****************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (647 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 12.77
//
[ok]

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

Downloads

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

Related tools

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