Alignments for a candidate for pcaF in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaF in Rhizorhabdus wittichii RW1

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_011951599.1 SWIT_RS03835 3-oxoadipyl-CoA thiolase

Query= metacyc::MONOMER-3207
         (400 letters)



>NCBI__GCF_000016765.1:WP_011951599.1
          Length = 399

 Score =  534 bits (1375), Expect = e-156
 Identities = 272/401 (67%), Positives = 324/401 (80%), Gaps = 3/401 (0%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M D +ICDA RTPIGR+GG+LA VRADDLAA+P++ L E NP +    +D++ FGCANQA
Sbjct: 1   MADAYICDAARTPIGRYGGSLAAVRADDLAAIPMRVLRERNPGIV-GHIDDILFGCANQA 59

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARMA LL+GL E  PG T+NRLC SGMDA+  A RAI +GE +L +AGGVESM
Sbjct: 60  GEDNRNVARMAALLSGLGEDAPGTTINRLCGSGMDAVAYAARAIKAGEADLIVAGGVESM 119

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           SRAPFVM KA+  +SR+  + DTTIGWRF+N LMK ++G+DSMPETA+NVA D+QVSR D
Sbjct: 120 SRAPFVMPKADGAFSRSNAVYDTTIGWRFVNKLMKERFGIDSMPETAENVAQDFQVSRED 179

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETI-VERDEHLRPETTLEALTKLKP 239
           QD FA+ SQ++AAAAQA G  A EIVPV I  +KG+ I V+RDEH R ET++EAL KLKP
Sbjct: 180 QDRFAVESQRRAAAAQANGRLAAEIVPVTIPQRKGDPIVVDRDEHPR-ETSMEALGKLKP 238

Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299
           +   D T+TAGNASGVNDGAAA+I+AS  AV+ +GLTPRA+VLG A  GV PR+MGIGP 
Sbjct: 239 IVRADGTITAGNASGVNDGAAAIIVASKAAVEAYGLTPRAKVLGGAVAGVPPRIMGIGPA 298

Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359
           PA +KL ERLG+ +   DV+ELNEAFASQGLAVLR+LG+ DDA  VNPNGGAIALGHPLG
Sbjct: 299 PASKKLLERLGIGIGAIDVVELNEAFASQGLAVLRQLGLPDDAAHVNPNGGAIALGHPLG 358

Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           MSGARLVLTA  +L +SG  K L TMC+GVGQG+ALAIERV
Sbjct: 359 MSGARLVLTATEELVRSGAGKALCTMCIGVGQGIALAIERV 399


Lambda     K      H
   0.318    0.134    0.383 

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: 526
Number of extensions: 17
Number of successful extensions: 2
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: 400
Length of database: 399
Length adjustment: 31
Effective length of query: 369
Effective length of database: 368
Effective search space:   135792
Effective search space used:   135792
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_011951599.1 SWIT_RS03835 (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.1876384.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-207  674.5  12.9   2.9e-207  674.4  12.9    1.0  1  NCBI__GCF_000016765.1:WP_011951599.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016765.1:WP_011951599.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  674.4  12.9  2.9e-207  2.9e-207       2     400 .]       3     399 .]       2     399 .] 0.99

  Alignments for each domain:
  == domain 1  score: 674.4 bits;  conditional E-value: 2.9e-207
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           ++yi+da rtpiGrygGsl++vraddlaa+p++ l +rnp + +  idd+++GcanqaGednrnvarmaall+
  NCBI__GCF_000016765.1:WP_011951599.1   3 DAYICDAARTPIGRYGGSLAAVRADDLAAIPMRVLRERNPGI-VGHIDDILFGCANQAGEDNRNVARMAALLS 74 
                                           69**************************************99.679*************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           Gl ++ pgtt+nrlcgsg+da+++aaraikaGeadl++aGGvesmsrapfv+ kad+afsrs+ + dttiGwr
  NCBI__GCF_000016765.1:WP_011951599.1  75 GLGEDAPGTTINRLCGSGMDAVAYAARAIKAGEADLIVAGGVESMSRAPFVMPKADGAFSRSNAVYDTTIGWR 147
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220
                                           fvn  +k+ +G+dsmpetaenva++f+vsredqd fa+ sq+r+aaaqa+G +a+eivpv+i+q+kG++ vvd
  NCBI__GCF_000016765.1:WP_011951599.1 148 FVNKLMKERFGIDSMPETAENVAQDFQVSREDQDRFAVESQRRAAAAQANGRLAAEIVPVTIPQRKGDPIVVD 220
                                           ************************************************************************* PP

                             TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293
                                           +deh+r et++eal klk++vr+dgt+taGnasGvndGaaa+++as+ av+++gltpra++l+ a aGv pr+
  NCBI__GCF_000016765.1:WP_011951599.1 221 RDEHPR-ETSMEALGKLKPIVRADGTITAGNASGVNDGAAAIIVASKAAVEAYGLTPRAKVLGGAVAGVPPRI 292
                                           ******.****************************************************************** PP

                             TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366
                                           mG+gp+pa kkll+r+g+ +  +dv+elneafa+q+lavlr+lgl+dd+a+vnpnGGaialGhplG+sGarlv
  NCBI__GCF_000016765.1:WP_011951599.1 293 MGIGPAPASKKLLERLGIGIGAIDVVELNEAFASQGLAVLRQLGLPDDAAHVNPNGGAIALGHPLGMSGARLV 365
                                           ************************************************************************* PP

                             TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400
                                           lta ++l +sg   al+t+ciGvGqGial+ierv
  NCBI__GCF_000016765.1:WP_011951599.1 366 LTATEELVRSGAGKALCTMCIGVGQGIALAIERV 399
                                           *********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (399 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: 29.23
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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