Alignments for a candidate for pcaF in Mesorhizobium ciceri WSM1271

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaF in Mesorhizobium ciceri WSM1271

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate YP_004140309.1 Mesci_1095 beta-ketoadipyl CoA thiolase

Query= metacyc::MONOMER-15952
         (401 letters)



>NCBI__GCF_000185905.1:YP_004140309.1
          Length = 401

 Score =  565 bits (1456), Expect = e-166
 Identities = 284/401 (70%), Positives = 334/401 (83%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M EA I D +RTPIGR+ G+L+SVR+DDLGAIPL+AL  R+P +DW A+DDV+YGCANQA
Sbjct: 1   MAEAYICDYIRTPIGRFGGSLSSVRSDDLGAIPLRALAERNPGIDWQAIDDVVYGCANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARMA LLAGLP  VPG+T+NRLCGSG+DA+  AARA++ GEA LM+AGGVESM
Sbjct: 61  GEDNRNVARMALLLAGLPKEVPGSTVNRLCGSGMDALTIAARAIKAGEAELMIAGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           SRAPFVM K++ AF R+AEI+DTTIGWRFVN LM++ +G+DSMPET ENVA  F++SRAD
Sbjct: 121 SRAPFVMPKADTAFSRNAEIYDTTIGWRFVNPLMKKQYGVDSMPETGENVAEDFSVSRAD 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QDAFA+RSQ+KA AA ANGRLAKEI  V I QRKG A IV  DEHPR  +T+E LAKL T
Sbjct: 181 QDAFAVRSQNKAVAAQANGRLAKEITPVTILQRKGDALIVSKDEHPRAGSTVEALAKLPT 240

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
           PFRQGG+VTAGNASGVNDGA AL++AS  A +++GL   AR++G A AGV PRIMGIGPV
Sbjct: 241 PFRQGGTVTAGNASGVNDGAAALIVASEAAVKKYGLTPIARILGGAAAGVAPRIMGIGPV 300

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PAT+K+    GL     DVIELNEAFA+QG+AVLR+LG+A+D E VNPNGGAIALGHPLG
Sbjct: 301 PATQKLCARLGLTPKQFDVIELNEAFASQGIAVLRQLGIAEDAEHVNPNGGAIALGHPLG 360

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           MSGAR+  TA  EL ER GRYAL TMCIGVGQGIA+ +ER+
Sbjct: 361 MSGARISGTAALELRERGGRYALATMCIGVGQGIAIALERV 401


Lambda     K      H
   0.319    0.134    0.384 

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: 577
Number of extensions: 13
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 YP_004140309.1 Mesci_1095 (beta-ketoadipyl 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.4095019.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-215  701.5   8.9   1.9e-215  701.3   8.9    1.0  1  NCBI__GCF_000185905.1:YP_004140309.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000185905.1:YP_004140309.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  701.3   8.9  1.9e-215  1.9e-215       2     400 .]       3     401 .]       2     401 .] 1.00

  Alignments for each domain:
  == domain 1  score: 701.3 bits;  conditional E-value: 1.9e-215
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           e+yi+d irtpiGr+gGslssvr+ddl+a+pl+al +rnp +d++aiddv++GcanqaGednrnvarma+lla
  NCBI__GCF_000185905.1:YP_004140309.1   3 EAYICDYIRTPIGRFGGSLSSVRSDDLGAIPLRALAERNPGIDWQAIDDVVYGCANQAGEDNRNVARMALLLA 75 
                                           79*********************************************************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           Glp++vpg+tvnrlcgsg+dal++aaraikaGea+l+iaGGvesmsrapfv+ kad+afsr+a++ dttiGwr
  NCBI__GCF_000185905.1:YP_004140309.1  76 GLPKEVPGSTVNRLCGSGMDALTIAARAIKAGEAELMIAGGVESMSRAPFVMPKADTAFSRNAEIYDTTIGWR 148
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220
                                           fvnp +k++yGvdsmpet envae+f+vsr+dqdafa+rsq+++ aaqa+G +a+ei+pv+i q+kG++ +v+
  NCBI__GCF_000185905.1:YP_004140309.1 149 FVNPLMKKQYGVDSMPETGENVAEDFSVSRADQDAFAVRSQNKAVAAQANGRLAKEITPVTILQRKGDALIVS 221
                                           ************************************************************************* PP

                             TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293
                                           kdeh+ra +t+ealakl +++r++gtvtaGnasGvndGaaal++ase avk++gltp aril+ a+aGv+pr+
  NCBI__GCF_000185905.1:YP_004140309.1 222 KDEHPRAGSTVEALAKLPTPFRQGGTVTAGNASGVNDGAAALIVASEAAVKKYGLTPIARILGGAAAGVAPRI 294
                                           ************************************************************************* PP

                             TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366
                                           mG+gpvpa++kl ar+gl+ +++dvielneafa+q++avlr+lg+a+d+++vnpnGGaialGhplG+sGar+ 
  NCBI__GCF_000185905.1:YP_004140309.1 295 MGIGPVPATQKLCARLGLTPKQFDVIELNEAFASQGIAVLRQLGIAEDAEHVNPNGGAIALGHPLGMSGARIS 367
                                           ************************************************************************* PP

                             TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400
                                            ta  +l+++ggryalat+ciGvGqGia+++erv
  NCBI__GCF_000185905.1:YP_004140309.1 368 GTAALELRERGGRYALATMCIGVGQGIAIALERV 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 24.09
//
[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