Alignments for a candidate for pcaB in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Pseudomonas fluorescens GW456-L13

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate PfGW456L13_4586 3-carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2)

Query= uniprot:A0A0C4YE08
         (470 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4586
          Length = 454

 Score =  445 bits (1144), Expect = e-129
 Identities = 231/445 (51%), Positives = 296/445 (66%), Gaps = 4/445 (0%)

Query: 5   SRLTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGEI 64
           ++L D  F +      F D   VQ MLDFEAALARAEA  G+IP+ A   I A CRAG  
Sbjct: 7   NQLFDAYFTARDMREVFCDQGRVQAMLDFEAALARAEARVGMIPSSAVAPIEAACRAGLY 66

Query: 65  DFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQLREAL 124
           DF  L  A    GN AIPLV+ L  ++AA DA+A RYVH GATSQD +D+G+VLQLR AL
Sbjct: 67  DFAMLGEAIATAGNSAIPLVKALGKQIAATDAEAERYVHLGATSQDVMDSGLVLQLRRAL 126

Query: 125 QAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRLDA 184
           + +++DL  LG   A+ A ++  TP+  RTWLQHA P T G+K AGWL A+ R  +RL  
Sbjct: 127 ELIESDLAQLGQTLASQAQRYATTPLAGRTWLQHATPVTLGMKIAGWLGAVTRSRQRLAE 186

Query: 185 ARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVATTLGM 244
            + +   LQFGGA+GTLA+LG  A  +A AL   L L +   PWH  RDR+VE    LG+
Sbjct: 187 LKPRLLVLQFGGASGTLAALGEQAMPIAQALAEELQLTLPDQPWHTQRDRVVEFGAALGL 246

Query: 245 LTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRVPPLV 304
           + GSLGK+ RD+SL+MQTE AEV EP+ PG+GGSSTMPHKRNPVG A ++ AA RVP L+
Sbjct: 247 IAGSLGKLGRDISLLMQTEAAEVFEPSAPGKGGSSTMPHKRNPVGAAVLIGAATRVPGLL 306

Query: 305 ATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLGVT 364
           +T+ + M QEHER+LG W AEW+TLP+I  L +G+L Q L +V GL+VDA RM  NL +T
Sbjct: 307 STLFSAMPQEHERSLGLWHAEWETLPEICCLVSGSLHQALLIVQGLEVDAERMARNLDLT 366

Query: 365 HGLILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAGLMDA 424
            GL+LAEA  + L  ++GR  AHHL+E  C+RAVAE   LR  LG    ++      + A
Sbjct: 367 QGLVLAEAVSIVLAQRVGRNTAHHLLEQCCKRAVAEQRHLRAVLG----DEPQVTAELSA 422

Query: 425 AALDRVCDPANYAGQAAGFVDAVLA 449
           A LD + D A+Y GQA  +V+  +A
Sbjct: 423 AELDHLLDSAHYLGQAKTWVERAVA 447


Lambda     K      H
   0.319    0.130    0.380 

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: 454
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: 470
Length of database: 454
Length adjustment: 33
Effective length of query: 437
Effective length of database: 421
Effective search space:   183977
Effective search space used:   183977
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: 51 (24.3 bits)

Align candidate PfGW456L13_4586 (3-carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2))
to HMM TIGR02426 (pcaB: 3-carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2))

# 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/TIGR02426.hmm
# target sequence database:        /tmp/gapView.22647.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02426  [M=338]
Accession:   TIGR02426
Description: protocat_pcaB: 3-carboxy-cis,cis-muconate cycloisomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   2.5e-144  466.3  10.2   3.4e-144  465.9  10.2    1.2  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4586  3-carboxy-cis,cis-muconate cyclo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4586  3-carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.9  10.2  3.4e-144  3.4e-144       1     338 []       9     352 ..       9     352 .. 0.99

  Alignments for each domain:
  == domain 1  score: 465.9 bits;  conditional E-value: 3.4e-144
                                               TIGR02426   1 lldglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaae 55 
                                                             l+d++f++ +++e+f d++r++amld+Eaalara+a+vG+ip++a++ i+aa+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4586   9 LFDAYFTARDMREVFCDQGRVQAMLDFEAALARAEARVGMIPSSAVAPIEAACRA 63 
                                                             7899*************************************************** PP

                                               TIGR02426  56 lalDlealaeaaaeagnvviplvkalrkavae...eaaryvHlGaTSQDviDTal 107
                                                               +D + l ea+a+agn++iplvkal k++a+   ea+ryvHlGaTSQDv+D +l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4586  64 GLYDFAMLGEAIATAGNSAIPLVKALGKQIAAtdaEAERYVHLGATSQDVMDSGL 118
                                                             ******************************999999******************* PP

                                               TIGR02426 108 mLqlrdaldllladlerlaeaLaelaarhrdtpltarTllQqAvpttvglkaagw 162
                                                             +Lqlr+al+l++ dl++l ++La++a+r + tpl +rT+lQ+A+p+t+g+k+agw
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4586 119 VLQLRRALELIESDLAQLGQTLASQAQRYATTPLAGRTWLQHATPVTLGMKIAGW 173
                                                             ******************************************************* PP

                                               TIGR02426 163 laavlrardrlealrtealalqfGGAaGtlaalekkglavaealAaelgLeapal 217
                                                             l av+r+r+rl++l+ ++l+lqfGGA+Gtlaal+++++ +a+alA+el+L++p +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4586 174 LGAVTRSRQRLAELKPRLLVLQFGGASGTLAALGEQAMPIAQALAEELQLTLPDQ 228
                                                             ******************************************************* PP

                                               TIGR02426 218 pWhtqrdriaelaaaLalvagalgkiaqDvallaqtevgevle.agg..GGSSam 269
                                                             pWhtqrdr++e++aaL+l+ag+lgk+++D++ll+qte++ev+e +++  GGSS+m
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4586 229 PWHTQRDRVVEFGAALGLIAGSLGKLGRDISLLMQTEAAEVFEpSAPgkGGSSTM 283
                                                             *******************************************766689****** PP

                                               TIGR02426 270 pHKrNPvaaevlaaaarrapglvatLfaalaqedeRsaggWhaeWetLrelvalt 324
                                                             pHKrNPv+a+vl++aa+r+pgl++tLf+a++qe+eRs+g WhaeWetL+e+++l+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4586 284 PHKRNPVGAAVLIGAATRVPGLLSTLFSAMPQEHERSLGLWHAEWETLPEICCLV 338
                                                             ******************************************************* PP

                                               TIGR02426 325 agalrqaaellegl 338
                                                             +g+l+qa  +++gl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4586 339 SGSLHQALLIVQGL 352
                                                             *******9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (454 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: 00:00:00.01
# Mc/sec: 9.67
//
[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:

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