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.4095679.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: 22.13
//
[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:

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:

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:

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:

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