GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Halomonas desiderata SP1

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_010626093.1 BZY95_RS06835 3-oxoadipyl-CoA thiolase

Query= metacyc::MONOMER-15952
         (401 letters)



>NCBI__GCF_002151265.1:WP_010626093.1
          Length = 401

 Score =  635 bits (1639), Expect = 0.0
 Identities = 324/401 (80%), Positives = 351/401 (87%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M +ALIIDA+RTPIGRY GALASVRADDLGA+PL+AL+ARHP LDW  VDD+ YGCANQA
Sbjct: 1   MKDALIIDAIRTPIGRYGGALASVRADDLGAVPLRALMARHPSLDWRQVDDIFYGCANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARM+ALLAGLPV VPGTT NRLCGSGLDAVG+AARA++ GEAGLM+AGGVESM
Sbjct: 61  GEDNRNVARMSALLAGLPVEVPGTTFNRLCGSGLDAVGNAARAIKTGEAGLMIAGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           SRAPFVMGK+EQAF RSAEIFDTTIGWRFVN+ M+  FGIDSMPETAENVA QF ISR D
Sbjct: 121 SRAPFVMGKAEQAFSRSAEIFDTTIGWRFVNRQMKAQFGIDSMPETAENVAEQFAISRED 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QD FALRSQ + AAA+  GRLA EIV VE+A+RK    +V+ DEHPR  TTLEQLA L T
Sbjct: 181 QDLFALRSQQRTAAAMEAGRLAAEIVPVEVARRKQAPLVVDTDEHPRAATTLEQLAGLPT 240

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
           PFR+ GSVTAGNASGVNDGACALLLAS+E A+R GL+ RARVVGMAT GVEPRIMG GP 
Sbjct: 241 PFREDGSVTAGNASGVNDGACALLLASAEQAERFGLEPRARVVGMATVGVEPRIMGFGPA 300

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PATRKVL  TGL+L  MDVIELNEAFAAQ LAV R LGL DD E VNPNGGAIALGHPLG
Sbjct: 301 PATRKVLTQTGLSLEQMDVIELNEAFAAQALAVTRNLGLPDDAEHVNPNGGAIALGHPLG 360

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           MSGARLVTTAL+ELE RQGRYALCTMCIGVGQGIALIIER+
Sbjct: 361 MSGARLVTTALYELERRQGRYALCTMCIGVGQGIALIIERL 401


Lambda     K      H
   0.319    0.134    0.384 

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: 600
Number of extensions: 15
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: 401
Length of database: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_010626093.1 BZY95_RS06835 (3-oxoadipyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

# 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/TIGR02430.hmm
# target sequence database:        /tmp/gapView.22567.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02430  [M=400]
Accession:   TIGR02430
Description: pcaF: 3-oxoadipyl-CoA thiolase
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-223  728.5   7.7   1.1e-223  728.4   7.7    1.0  1  lcl|NCBI__GCF_002151265.1:WP_010626093.1  BZY95_RS06835 3-oxoadipyl-CoA th


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_010626093.1  BZY95_RS06835 3-oxoadipyl-CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  728.4   7.7  1.1e-223  1.1e-223       1     400 []       2     401 .]       2     401 .] 1.00

  Alignments for each domain:
  == domain 1  score: 728.4 bits;  conditional E-value: 1.1e-223
                                 TIGR02430   1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarm 69 
                                               k++ i+dairtpiGrygG+l+svraddl+avpl+al+ar+psld+ ++dd+++GcanqaGednrnvarm
  lcl|NCBI__GCF_002151265.1:WP_010626093.1   2 KDALIIDAIRTPIGRYGGALASVRADDLGAVPLRALMARHPSLDWRQVDDIFYGCANQAGEDNRNVARM 70 
                                               5789***************************************************************** PP

                                 TIGR02430  70 aallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsak 138
                                               +allaGlpv+vpgtt nrlcgsglda+g aaraik+Gea l+iaGGvesmsrapfv+Gka+ afsrsa+
  lcl|NCBI__GCF_002151265.1:WP_010626093.1  71 SALLAGLPVEVPGTTFNRLCGSGLDAVGNAARAIKTGEAGLMIAGGVESMSRAPFVMGKAEQAFSRSAE 139
                                               ********************************************************************* PP

                                 TIGR02430 139 ledttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpv 207
                                               ++dttiGwrfvn ++ka++G+dsmpetaenvae+f++sredqd falrsqqrtaaa ++G +a+eivpv
  lcl|NCBI__GCF_002151265.1:WP_010626093.1 140 IFDTTIGWRFVNRQMKAQFGIDSMPETAENVAEQFAISREDQDLFALRSQQRTAAAMEAGRLAAEIVPV 208
                                               ********************************************************************* PP

                                 TIGR02430 208 eikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhglt 276
                                               e++++k  + vvd+deh+ra ttle+la l +++redg+vtaGnasGvndGa+alllas+e ++r+gl 
  lcl|NCBI__GCF_002151265.1:WP_010626093.1 209 EVARRKQAPLVVDTDEHPRAATTLEQLAGLPTPFREDGSVTAGNASGVNDGACALLLASAEQAERFGLE 277
                                               ********************************************************************* PP

                                 TIGR02430 277 prarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarv 345
                                               prar++++a++Gvepr+mG+gp+pa++k+l+++glsle++dvielneafaaqalav+r+lgl+dd+++v
  lcl|NCBI__GCF_002151265.1:WP_010626093.1 278 PRARVVGMATVGVEPRIMGFGPAPATRKVLTQTGLSLEQMDVIELNEAFAAQALAVTRNLGLPDDAEHV 346
                                               ********************************************************************* PP

                                 TIGR02430 346 npnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400
                                               npnGGaialGhplG+sGarlv+tal++le+++gryal+t+ciGvGqGial+ier+
  lcl|NCBI__GCF_002151265.1:WP_010626093.1 347 NPNGGAIALGHPLGMSGARLVTTALYELERRQGRYALCTMCIGVGQGIALIIERL 401
                                               *****************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (401 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: 00:00:00.01
# Mc/sec: 10.33
//
[ok]

This GapMind analysis is from Sep 24 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:

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