GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Cupriavidus basilensis 4G11

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate RR42_RS35915 RR42_RS35915 beta-ketoadipyl CoA thiolase

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



>FitnessBrowser__Cup4G11:RR42_RS35915
          Length = 400

 Score =  585 bits (1507), Expect = e-171
 Identities = 292/401 (72%), Positives = 339/401 (84%), Gaps = 1/401 (0%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M EA I DA+RTPIGRYAG+L+ VR DDLGA+PLKAL+AR+P LDWSA+DDVIYG ANQA
Sbjct: 1   MTEAFICDAIRTPIGRYAGSLSGVRPDDLGAVPLKALMARNPNLDWSAIDDVIYGNANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARM+ LLAGLP SVPG T+NRLCGSG+DA G+AARA++ GEAGLMLAGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPQSVPGATINRLCGSGMDATGTAARAIKSGEAGLMLAGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           SRAPFVMGK+  AF R A+IFDTTIGWRF+N  M+  +G+DSMPETAENVA  + ISR D
Sbjct: 121 SRAPFVMGKATSAFSRDAQIFDTTIGWRFINPAMRAAYGVDSMPETAENVATDYKISRED 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QD  ALRSQ KA+ A A+G LA+EI AV IAQ+KG   +VE DEHPR  T++E L KL  
Sbjct: 181 QDLMALRSQEKASRAQADGTLAQEITAVTIAQKKGDPLVVERDEHPRA-TSMEALGKLRG 239

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
             R  G+VTAGNASGVNDGACA+LLAS  AA++HGL  +AR+VGMATAGV PR+MGIGP 
Sbjct: 240 VVRADGTVTAGNASGVNDGACAILLASEAAARQHGLTPKARIVGMATAGVAPRVMGIGPA 299

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PA++K+L+  G+ +  MDVIELNEAFAAQGLAVLRELG+ADDD RVNPNGGAIALGHPLG
Sbjct: 300 PASQKLLKQLGMTIDQMDVIELNEAFAAQGLAVLRELGVADDDARVNPNGGAIALGHPLG 359

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           MSGARLVTTA+++L    GRYALCTMCIGVGQGIA++IER+
Sbjct: 360 MSGARLVTTAMYQLHRTGGRYALCTMCIGVGQGIAMVIERV 400


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: 546
Number of extensions: 15
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: 401
Length of database: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
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 RR42_RS35915 RR42_RS35915 (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.23733.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-223  726.4  13.2   5.2e-223  726.2  13.2    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS35915  RR42_RS35915 beta-ketoadipyl CoA


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS35915  RR42_RS35915 beta-ketoadipyl CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  726.2  13.2  5.2e-223  5.2e-223       2     400 .]       3     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 726.2 bits;  conditional E-value: 5.2e-223
                                 TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarma 70 
                                               e++i+dairtpiGry+Gsls vr ddl+avplkal+arnp+ld++aiddvi+G anqaGednrnvarm+
  lcl|FitnessBrowser__Cup4G11:RR42_RS35915   3 EAFICDAIRTPIGRYAGSLSGVRPDDLGAVPLKALMARNPNLDWSAIDDVIYGNANQAGEDNRNVARMS 71 
                                               89******************************************************************* PP

                                 TIGR02430  71 allaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakl 139
                                               +llaGlp+svpg+t+nrlcgsg+da g+aaraik+Gea l++aGGvesmsrapfv+Gka safsr+a++
  lcl|FitnessBrowser__Cup4G11:RR42_RS35915  72 LLLAGLPQSVPGATINRLCGSGMDATGTAARAIKSGEAGLMLAGGVESMSRAPFVMGKATSAFSRDAQI 140
                                               ********************************************************************* PP

                                 TIGR02430 140 edttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpve 208
                                               +dttiGwrf+np+++a yGvdsmpetaenva+++++sredqd +alrsq+++++aqa G +a+ei+ v+
  lcl|FitnessBrowser__Cup4G11:RR42_RS35915 141 FDTTIGWRFINPAMRAAYGVDSMPETAENVATDYKISREDQDLMALRSQEKASRAQADGTLAQEITAVT 209
                                               ********************************************************************* PP

                                 TIGR02430 209 ikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltp 277
                                               i+qkkG++ vv++deh+r  t++eal kl++vvr+dgtvtaGnasGvndGa+a+llase a+++hgltp
  lcl|FitnessBrowser__Cup4G11:RR42_RS35915 210 IAQKKGDPLVVERDEHPR-ATSMEALGKLRGVVRADGTVTAGNASGVNDGACAILLASEAAARQHGLTP 277
                                               ******************.8************************************************* PP

                                 TIGR02430 278 rarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvn 346
                                               +ari+++a+aGv+prvmG+gp+pa +kll+++g++++++dvielneafaaq+lavlrelg+adddarvn
  lcl|FitnessBrowser__Cup4G11:RR42_RS35915 278 KARIVGMATAGVAPRVMGIGPAPASQKLLKQLGMTIDQMDVIELNEAFAAQGLAVLRELGVADDDARVN 346
                                               ********************************************************************* PP

                                 TIGR02430 347 pnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400
                                               pnGGaialGhplG+sGarlv+ta++ql+++ggryal+t+ciGvGqGia+vierv
  lcl|FitnessBrowser__Cup4G11:RR42_RS35915 347 PNGGAIALGHPLGMSGARLVTTAMYQLHRTGGRYALCTMCIGVGQGIAMVIERV 400
                                               *****************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (400 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.99
//
[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:

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