GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_068168283.1 HTA01S_RS06660 acetyl-CoA C-acetyltransferase

Query= SwissProt::P14611
         (393 letters)



>NCBI__GCF_001592305.1:WP_068168283.1
          Length = 392

 Score =  557 bits (1435), Expect = e-163
 Identities = 283/392 (72%), Positives = 325/392 (82%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           M D+VIVSAARTAVGKFGGSLAK PA ELG++VIK  L R G+  + V EVIMGQVL AG
Sbjct: 1   MEDIVIVSAARTAVGKFGGSLAKTPATELGSIVIKELLARTGLPVDAVGEVIMGQVLAAG 60

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
            GQNPARQA +KAG+    PA+TIN VCGSGLKAVMLAA A+  GD+EIV+AGGQENMSA
Sbjct: 61  CGQNPARQAMMKAGVAKETPALTINAVCGSGLKAVMLAAQAVAWGDSEIVIAGGQENMSA 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180
           +PHVL GSRDG RMGD K+ DTMIVDGLWDVYNQYHMGITAENVAK  GITRE QD  A 
Sbjct: 121 SPHVLNGSRDGQRMGDWKMTDTMIVDGLWDVYNQYHMGITAENVAKAQGITREMQDALAA 180

Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240
           GSQ KA AAQ AGKF +EIV V IPQRKGDPV F +DEF+    T + ++GL+PAFDK+G
Sbjct: 181 GSQQKAAAAQAAGKFKDEIVGVSIPQRKGDPVLFNSDEFINAKTTAEVLAGLRPAFDKSG 240

Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300
           +VTA NASG+NDGAAAV+VM+A KA  LGLTPLA I ++  +G+DP +MGMGPVPAS++A
Sbjct: 241 SVTAGNASGINDGAAAVMVMTAKKAAALGLTPLARIAAFGTSGLDPALMGMGPVPASQKA 300

Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360
           L+RA W   D+D+ E+NEAFAAQA AV+  +  D +KVNVNGGAIAIGHPIGASGCRILV
Sbjct: 301 LARAGWKASDVDVFELNEAFAAQACAVNMALDIDPAKVNVNGGAIAIGHPIGASGCRILV 360

Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
           TLLHEM+RR AKKGLA+LCIGGGMGV+LAVER
Sbjct: 361 TLLHEMQRRGAKKGLAALCIGGGMGVSLAVER 392


Lambda     K      H
   0.315    0.131    0.369 

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: 528
Number of extensions: 16
Number of successful extensions: 1
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: 393
Length of database: 392
Length adjustment: 31
Effective length of query: 362
Effective length of database: 361
Effective search space:   130682
Effective search space used:   130682
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_068168283.1 HTA01S_RS06660 (acetyl-CoA C-acetyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# 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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.1851374.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-144  468.1  15.0   1.2e-144  467.9  15.0    1.0  1  NCBI__GCF_001592305.1:WP_068168283.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001592305.1:WP_068168283.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.9  15.0  1.2e-144  1.2e-144       1     385 []       6     391 ..       6     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 467.9 bits;  conditional E-value: 1.2e-144
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           iv+a+Rt++gk+ggsl++++a +L++ vikell+r+gl  +++ evi+G+vl ag+++n+aR+a+++ag+ ++
  NCBI__GCF_001592305.1:WP_068168283.1   6 IVSAARTAVGKFGGSLAKTPATELGSIVIKELLARTGLPVDAVGEVIMGQVLAAGCGQNPARQAMMKAGVAKE 78 
                                           8************************************************************************ PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           +palt+n vC+Sgl+Av+laaq+++ G+ ++v+aGG E+mS +p++l+ s  r++ ++g+ k+ d+++ d+  
  NCBI__GCF_001592305.1:WP_068168283.1  79 TPALTINAVCGSGLKAVMLAAQAVAWGDSEIVIAGGQENMSASPHVLNGS--RDGQRMGDWKMTDTMIVDGlw 149
                                           ************************************************98..8*****************9** PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDegirp 213
                                            v+++++mg+tAen+ak  gi+Re+qD++a+ S+qkaa+A+++gkfkdeiv v+++++   ++ +++De i +
  NCBI__GCF_001592305.1:WP_068168283.1 150 dVYNQYHMGITAENVAKAQGITREMQDALAAGSQQKAAAAQAAGKFKDEIVGVSIPQRkgdPVLFNSDEFINA 222
                                           *99*****************************************************999*99*********** PP

                             TIGR01930 214 nttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgp 286
                                           +tt+e La+L+paf++ +gs vtAgN+s++nDGAaa+++m+ ++a++lgltplari +++++g+dp+ mg+gp
  NCBI__GCF_001592305.1:WP_068168283.1 223 KTTAEVLAGLRPAFDK-SGS-VTAGNASGINDGAAAVMVMTAKKAAALGLTPLARIAAFGTSGLDPALMGMGP 293
                                           **************95.8*7.**************************************************** PP

                             TIGR01930 287 vpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllke 359
                                           vpA++kaL++ag+++sd+d++E+nEAFAaq+ av+ +l+ +d++kvNvnGGAiA+GHP+GasG+ri++tll+e
  NCBI__GCF_001592305.1:WP_068168283.1 294 VPASQKALARAGWKASDVDVFELNEAFAAQACAVNMALD-IDPAKVNVNGGAIAIGHPIGASGCRILVTLLHE 365
                                           ***************************************.88******************************* PP

                             TIGR01930 360 LkergkkyGlatlCvggGqGaAvile 385
                                           +++rg+k Gla+lC+ggG+G+++ +e
  NCBI__GCF_001592305.1:WP_068168283.1 366 MQRRGAKKGLAALCIGGGMGVSLAVE 391
                                           *********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 19.64
//
[ok]

This GapMind analysis is from Apr 09 2024. 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