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_012050514.1 SWIT_RS21925 3-oxoadipyl-CoA thiolase

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



>NCBI__GCF_000016765.1:WP_012050514.1
          Length = 402

 Score =  553 bits (1424), Expect = e-162
 Identities = 272/402 (67%), Positives = 335/402 (83%), Gaps = 2/402 (0%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M + FICDA+RTPIGR+GG L+GVRADDL A+P++ALIE NP +    ++EVF+GCANQ+
Sbjct: 1   MAEAFICDAVRTPIGRYGGILSGVRADDLGALPIRALIERNPGLDPASIEEVFYGCANQS 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARM+LLLAGLP ++PGVTLNRLCASG++A+G A RAI +GEM+LA+AGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPTAVPGVTLNRLCASGLEAVGAAARAIRTGEMDLAVAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           +RAP V+GKA   + R+ KLEDTT+GWRF+NP + + +G ++MP TA+N+A+D+ +SRAD
Sbjct: 121 TRAPLVIGKAGGAFGRDQKLEDTTMGWRFVNPALDALHGTETMPRTAENLAEDHGISRAD 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRI-AHKKGETI-VERDEHLRPETTLEALTKLK 238
           QDAFALRSQQ+A AAQA GF AEEI+ V +   ++GET  V+ DEH R +TTL+ L KLK
Sbjct: 181 QDAFALRSQQRAVAAQANGFLAEEIIAVTVPGRRRGETSQVDTDEHPRADTTLDTLAKLK 240

Query: 239 PVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGP 298
           P+ GP  TVTAGNASG+NDGAAA+I+A   A +   LTPRAR+LGMAS GV PRVMGIGP
Sbjct: 241 PLFGPAGTVTAGNASGINDGAAAMIVAGEAAARAADLTPRARILGMASAGVDPRVMGIGP 300

Query: 299 VPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPL 358
           VPA +KL  RLG+++  FD IELNEAFASQ LAVLR LG+ DDAPQVNPNGGAIALGHPL
Sbjct: 301 VPATQKLLARLGLSIEAFDAIELNEAFASQSLAVLRGLGLPDDAPQVNPNGGAIALGHPL 360

Query: 359 GMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           GMSGAR+  + +HQLE++GGR GLAT+CVGVG GLALA+ERV
Sbjct: 361 GMSGARIAASLVHQLERTGGRLGLATLCVGVGMGLALAVERV 402


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: 585
Number of extensions: 19
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: 402
Length adjustment: 31
Effective length of query: 369
Effective length of database: 371
Effective search space:   136899
Effective search space used:   136899
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_012050514.1 SWIT_RS21925 (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.1878507.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-205  668.9  11.3   1.5e-205  668.7  11.3    1.0  1  NCBI__GCF_000016765.1:WP_012050514.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016765.1:WP_012050514.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  668.7  11.3  1.5e-205  1.5e-205       2     400 .]       3     402 .]       2     402 .] 0.99

  Alignments for each domain:
  == domain 1  score: 668.7 bits;  conditional E-value: 1.5e-205
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           e++i+da+rtpiGrygG ls vraddl+a+p++al++rnp ld a+i++v++Gcanq+Gednrnvarm++lla
  NCBI__GCF_000016765.1:WP_012050514.1   3 EAFICDAVRTPIGRYGGILSGVRADDLGALPIRALIERNPGLDPASIEEVFYGCANQSGEDNRNVARMSLLLA 75 
                                           79*********************************************************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           Glp++vpg+t+nrlc+sgl+a+g aarai++Ge dl +aGGvesm+rap v+Gka +af+r++kledtt+Gwr
  NCBI__GCF_000016765.1:WP_012050514.1  76 GLPTAVPGVTLNRLCASGLEAVGAAARAIRTGEMDLAVAGGVESMTRAPLVIGKAGGAFGRDQKLEDTTMGWR 148
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikq.kkGeetvv 219
                                           fvnp+l al+G+++mp taen+ae++g+sr+dqdafalrsqqr+ aaqa+Gf+aeei+ v++++ ++Ge++ v
  NCBI__GCF_000016765.1:WP_012050514.1 149 FVNPALDALHGTETMPRTAENLAEDHGISRADQDAFALRSQQRAVAAQANGFLAEEIIAVTVPGrRRGETSQV 221
                                           **************************************************************972579***** PP

                             TIGR02430 220 dkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGvepr 292
                                           d+deh+ra+ttl++laklk+++ + gtvtaGnasG+ndGaaa+++a+e a+++ +ltpraril++asaGv+pr
  NCBI__GCF_000016765.1:WP_012050514.1 222 DTDEHPRADTTLDTLAKLKPLFGPAGTVTAGNASGINDGAAAMIVAGEAAARAADLTPRARILGMASAGVDPR 294
                                           ************************************************************************* PP

                             TIGR02430 293 vmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarl 365
                                           vmG+gpvpa++kllar+gls+e +d+ielneafa+q+lavlr lgl+dd+ +vnpnGGaialGhplG+sGar+
  NCBI__GCF_000016765.1:WP_012050514.1 295 VMGIGPVPATQKLLARLGLSIEAFDAIELNEAFASQSLAVLRGLGLPDDAPQVNPNGGAIALGHPLGMSGARI 367
                                           ************************************************************************* PP

                             TIGR02430 366 vltalkqleksggryalatlciGvGqGialvierv 400
                                           ++++++qle++ggr +latlc+GvG G+al++erv
  NCBI__GCF_000016765.1:WP_012050514.1 368 AASLVHQLERTGGRLGLATLCVGVGMGLALAVERV 402
                                           **********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (402 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: 00:00:00.00
# Mc/sec: 17.03
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 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