Alignments for a candidate for paaJ2 in Dechloromonas agitata is5

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Dechloromonas agitata is5

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_027456470.1 K420_RS0101365 3-oxoadipyl-CoA thiolase

Query= uniprot:D8ITH5
         (401 letters)



>NCBI__GCF_000519045.1:WP_027456470.1
          Length = 401

 Score =  630 bits (1625), Expect = 0.0
 Identities = 317/399 (79%), Positives = 350/399 (87%)

Query: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61
           +A ICDAIRTP GRYGG L  VRADDL A P+++LMERNP VDW+ V+DI+YGCANQAGE
Sbjct: 3   QAFICDAIRTPIGRYGGGLAGVRADDLGAIPLKALMERNPQVDWTAVDDIIYGCANQAGE 62

Query: 62  DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121
           DNRNVARM+GLLAGLPI VPG+TVNRLCGS +DAVG+AAR+IKSGE +LMIAGGVESM+R
Sbjct: 63  DNRNVARMSGLLAGLPIEVPGTTVNRLCGSGMDAVGLAARSIKSGETRLMIAGGVESMSR 122

Query: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181
           APFVMGKAE+A++R AAI+DTTIGWRF NPLMK  Y   SMP+TA+NVA +F I+RADQD
Sbjct: 123 APFVMGKAETAWSRQAAIYDTTIGWRFPNPLMKKLYDTHSMPQTADNVAEEFSISRADQD 182

Query: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241
           AFALRSQQRWAAA AAG FA E+ P+ IPQKKGD  VV TDEHPRPDTTL  LAKLKGV 
Sbjct: 183 AFALRSQQRWAAAHAAGRFADELVPVVIPQKKGDAKVVDTDEHPRPDTTLEMLAKLKGVN 242

Query: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301
            P+ +VTAGNASGVNDGACALLLAS  AA  Y L+P ARV+GMATAGV PRIMGFGPAPA
Sbjct: 243 GPELSVTAGNASGVNDGACALLLASEAAAGQYGLQPLARVVGMATAGVPPRIMGFGPAPA 302

Query: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361
           VRKVLAQ GLTLAQMDVIELNEAFAAQGLAV+RDLGL DD A VNPNGGAIA+GHPLG S
Sbjct: 303 VRKVLAQTGLTLAQMDVIELNEAFAAQGLAVLRDLGLADDEARVNPNGGAIALGHPLGMS 362

Query: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
           GARLVTTA  +L+R GGRYALCTMCIGVGQGIA+VIERV
Sbjct: 363 GARLVTTAAYELKRRGGRYALCTMCIGVGQGIAMVIERV 401


Lambda     K      H
   0.320    0.135    0.394 

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: 599
Number of extensions: 14
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_027456470.1 K420_RS0101365 (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.4327.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-223  728.5   6.8   1.2e-223  728.3   6.8    1.0  1  lcl|NCBI__GCF_000519045.1:WP_027456470.1  K420_RS0101365 3-oxoadipyl-CoA t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000519045.1:WP_027456470.1  K420_RS0101365 3-oxoadipyl-CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  728.3   6.8  1.2e-223  1.2e-223       2     400 .]       3     401 .]       2     401 .] 1.00

  Alignments for each domain:
  == domain 1  score: 728.3 bits;  conditional E-value: 1.2e-223
                                 TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarma 70 
                                               +++i+dairtpiGrygG+l+ vraddl+a+plkal++rnp++d++a+dd+i+GcanqaGednrnvarm+
  lcl|NCBI__GCF_000519045.1:WP_027456470.1   3 QAFICDAIRTPIGRYGGGLAGVRADDLGAIPLKALMERNPQVDWTAVDDIIYGCANQAGEDNRNVARMS 71 
                                               79******************************************************************* PP

                                 TIGR02430  71 allaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakl 139
                                                llaGlp +vpgttvnrlcgsg+da+glaar+ik+Ge+ l+iaGGvesmsrapfv+Gka++a+sr+a +
  lcl|NCBI__GCF_000519045.1:WP_027456470.1  72 GLLAGLPIEVPGTTVNRLCGSGMDAVGLAARSIKSGETRLMIAGGVESMSRAPFVMGKAETAWSRQAAI 140
                                               ********************************************************************* PP

                                 TIGR02430 140 edttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpve 208
                                                dttiGwrf np +k+ly ++smp+ta+nvaeef++sr+dqdafalrsqqr+aaa+a+G fa+e+vpv+
  lcl|NCBI__GCF_000519045.1:WP_027456470.1 141 YDTTIGWRFPNPLMKKLYDTHSMPQTADNVAEEFSISRADQDAFALRSQQRWAAAHAAGRFADELVPVV 209
                                               ********************************************************************* PP

                                 TIGR02430 209 ikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltp 277
                                               i+qkkG+++vvd+deh+r++ttle+laklk+v+ ++ +vtaGnasGvndGa+alllase a+ ++gl+p
  lcl|NCBI__GCF_000519045.1:WP_027456470.1 210 IPQKKGDAKVVDTDEHPRPDTTLEMLAKLKGVNGPELSVTAGNASGVNDGACALLLASEAAAGQYGLQP 278
                                               ********************************************************************* PP

                                 TIGR02430 278 rarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvn 346
                                                ar++++a+aGv pr+mG+gp+pav+k+la++gl+l+++dvielneafaaq+lavlr+lgladd+arvn
  lcl|NCBI__GCF_000519045.1:WP_027456470.1 279 LARVVGMATAGVPPRIMGFGPAPAVRKVLAQTGLTLAQMDVIELNEAFAAQGLAVLRDLGLADDEARVN 347
                                               ********************************************************************* PP

                                 TIGR02430 347 pnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400
                                               pnGGaialGhplG+sGarlv+ta ++l+++ggryal+t+ciGvGqGia+vierv
  lcl|NCBI__GCF_000519045.1:WP_027456470.1 348 PNGGAIALGHPLGMSGARLVTTAAYELKRRGGRYALCTMCIGVGQGIAMVIERV 401
                                               *****************************************************8 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: 00:00:00.04
# Mc/sec: 3.87
//
[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:

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