Alignments for a candidate for paaJ2 in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Halomonas desiderata SP1

Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_010626093.1 BZY95_RS06835 3-oxoadipyl-CoA thiolase

Query= reanno::Marino:GFF2751
         (415 letters)



>NCBI__GCF_002151265.1:WP_010626093.1
          Length = 401

 Score =  642 bits (1655), Expect = 0.0
 Identities = 325/406 (80%), Positives = 359/406 (88%), Gaps = 6/406 (1%)

Query: 7   LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66
           +KDA I+DAIRTPIGRYGGAL++VRADDLGA+P++AL  R+P LDW ++DD+ YGCANQA
Sbjct: 1   MKDALIIDAIRTPIGRYGGALASVRADDLGAVPLRALMARHPSLDWRQVDDIFYGCANQA 60

Query: 67  GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126
           GEDNR+VARMS LLAGLPV+VPG+T NRLCGSG+DAVG+AARAI+TGE  LMIAGGVESM
Sbjct: 61  GEDNRNVARMSALLAGLPVEVPGTTFNRLCGSGLDAVGNAARAIKTGEAGLMIAGGVESM 120

Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRED 186
           SRAPFVMGKA+ AFSR AEIFDTTIGWRFVN  +K Q+GIDSMPETAENVA  F ISRED
Sbjct: 121 SRAPFVMGKAEQAFSRSAEIFDTTIGWRFVNRQMKAQFGIDSMPETAENVAEQFAISRED 180

Query: 187 QDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPR-ETSLEKLASLPT 245
           QD FALRSQQRTAAA + GRLAAEI PV + RRKQ PLVVDTDEHPR  T+LE+LA LPT
Sbjct: 181 QDLFALRSQQRTAAAMEAGRLAAEIVPVEVARRKQAPLVVDTDEHPRAATTLEQLAGLPT 240

Query: 246 PFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPA 305
           PFRE+G+VTAGNASGVNDGACALLLA A+  +++ L+PRARVV MAT GVEPRIMGFGPA
Sbjct: 241 PFREDGSVTAGNASGVNDGACALLLASAEQAERFGLEPRARVVGMATVGVEPRIMGFGPA 300

Query: 306 PATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLG 365
           PATRKVL   GL L  MDVIELNEAFAAQALAVTR+LGLPDDAEHVNPNGGAIALGHPLG
Sbjct: 301 PATRKVLTQTGLSLEQMDVIELNEAFAAQALAVTRNLGLPDDAEHVNPNGGAIALGHPLG 360

Query: 366 MSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERM 411
           MSGARLVTTAL ELERR     + RYALCTMCIGVGQGIALIIER+
Sbjct: 361 MSGARLVTTALYELERR-----QGRYALCTMCIGVGQGIALIIERL 401


Lambda     K      H
   0.318    0.133    0.382 

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: 591
Number of extensions: 13
Number of successful extensions: 3
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: 415
Length of database: 401
Length adjustment: 31
Effective length of query: 384
Effective length of database: 370
Effective search space:   142080
Effective search space used:   142080
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: 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.4657.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.50
//
[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