Alignments for a candidate for paaJ2 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Herbaspirillum seropedicae SmR1

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate HSERO_RS20660 HSERO_RS20660 acetyl-CoA acetyltransferase

Query= uniprot:D8ITH5
         (401 letters)



>FitnessBrowser__HerbieS:HSERO_RS20660
          Length = 401

 Score =  786 bits (2029), Expect = 0.0
 Identities = 401/401 (100%), Positives = 401/401 (100%)

Query: 1   MEALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAG 60
           MEALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAG
Sbjct: 1   MEALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAG 60

Query: 61  EDNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMT 120
           EDNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMT
Sbjct: 61  EDNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMT 120

Query: 121 RAPFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180
           RAPFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ
Sbjct: 121 RAPFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180

Query: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240
           DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV
Sbjct: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240

Query: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300
           VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP
Sbjct: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300

Query: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360
           AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA
Sbjct: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360

Query: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERVA 401
           SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERVA
Sbjct: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERVA 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: 710
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 HSERO_RS20660 HSERO_RS20660 (acetyl-CoA acetyltransferase)
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.9550.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   7.1e-225  732.4   9.9   7.9e-225  732.2   9.9    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS20660  HSERO_RS20660 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS20660  HSERO_RS20660 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  732.2   9.9  7.9e-225  7.9e-225       2     400 .]       2     400 ..       1     400 [. 1.00

  Alignments for each domain:
  == domain 1  score: 732.2 bits;  conditional E-value: 7.9e-225
                                  TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarm 69 
                                                e+ i+dairtp+GrygG+l +vraddlaa p++ l++rnp +d++ ++d+++GcanqaGednrnvarm
  lcl|FitnessBrowser__HerbieS:HSERO_RS20660   2 EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGEDNRNVARM 69 
                                                789***************************************************************** PP

                                  TIGR02430  70 aallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsa 137
                                                a llaGlp +vpg+tvnrlcgs+lda+g+aaraik+Ge +l+iaGGvesm+rapfv+Gka+saf+rsa
  lcl|FitnessBrowser__HerbieS:HSERO_RS20660  70 AGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRAPFVMGKAESAFARSA 137
                                                ******************************************************************** PP

                                  TIGR02430 138 kledttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeiv 205
                                                 ++dttiGwrfvnp +ka+yG+dsmpetaenva++f+++r+dqdafalrsqqr+aaaqa+Gffa ei+
  lcl|FitnessBrowser__HerbieS:HSERO_RS20660 138 AIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQDAFALRSQQRWAAAQAAGFFAGEIA 205
                                                ******************************************************************** PP

                                  TIGR02430 206 pveikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrh 273
                                                p++i+qkkG++ vv +deh+r++ttl +laklk+vvr+dgtvtaGnasGvndGa+alllas +a+  +
  lcl|FitnessBrowser__HerbieS:HSERO_RS20660 206 PLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVVRPDGTVTAGNASGVNDGACALLLASPKAADLY 273
                                                ******************************************************************** PP

                                  TIGR02430 274 gltprarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladd 341
                                                +l+prar+l++a+aGv+pr+mG+gp+pav+k+la++gl+l+++dvielneafaaq+lav+r+lgl+dd
  lcl|FitnessBrowser__HerbieS:HSERO_RS20660 274 RLKPRARVLGMATAGVAPRIMGFGPAPAVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDD 341
                                                ******************************************************************** PP

                                  TIGR02430 342 darvnpnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400
                                                +a+vnpnGGaia+GhplGasGarlv+ta++qle+sggryal+t+ciGvGqGialvierv
  lcl|FitnessBrowser__HerbieS:HSERO_RS20660 342 AAHVNPNGGAIAIGHPLGASGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
                                                **********************************************************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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.45
//
[ok]

This GapMind analysis is from Sep 17 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