Alignments for a candidate for pcaB in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Pseudomonas fluorescens FW300-N2C3

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate AO356_04910 AO356_04910 3-carboxy-cis,cis-muconate cycloisomerase

Query= uniprot:A0A0C4YE08
         (470 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_04910
          Length = 454

 Score =  431 bits (1108), Expect = e-125
 Identities = 225/445 (50%), Positives = 291/445 (65%), Gaps = 4/445 (0%)

Query: 5   SRLTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGEI 64
           ++L D  F +      F D   VQ MLD EAALARAEA  G+IP  A  +I   CRA   
Sbjct: 7   NQLFDAYFTARDMREVFCDAGRVQAMLDVEAALARAEARVGLIPQSAVASIEKACRAEFY 66

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

Query: 125 QAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRLDA 184
             ++ +L  L    A  A ++  TP+  RTWLQHA P T G+K AGWL A+ R  +RL  
Sbjct: 127 GLIEGELAQLAAILARQAERYATTPLAGRTWLQHATPVTLGMKIAGWLGAITRSRQRLKE 186

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

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

Query: 305 ATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLGVT 364
           +T+ + M QEHER+LG W AEW+TLP+I  L +GAL+Q   +  GL+VDAARM  NL +T
Sbjct: 307 STLFSAMPQEHERSLGLWHAEWETLPEICCLVSGALQQARLLAEGLEVDAARMARNLELT 366

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

Query: 425 AALDRVCDPANYAGQAAGFVDAVLA 449
             +D + DPA+Y GQA  +V   +A
Sbjct: 423 TEIDHLLDPAHYLGQAQTWVVRAVA 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: 496
Number of extensions: 17
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 AO356_04910 AO356_04910 (3-carboxy-cis,cis-muconate cycloisomerase)
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.25587.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.2e-145  470.6   9.4   1.6e-145  470.2   9.4    1.2  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04910  AO356_04910 3-carboxy-cis,cis-mu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04910  AO356_04910 3-carboxy-cis,cis-muconate cycloisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.2   9.4  1.6e-145  1.6e-145       1     338 []       9     352 ..       9     352 .. 0.99

  Alignments for each domain:
  == domain 1  score: 470.2 bits;  conditional E-value: 1.6e-145
                                       TIGR02426   1 lldglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDleal 63 
                                                     l+d++f++ +++e+f d++r++amldvEaalara+a+vGlip++a+++i+ a+++  +D ++l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04910   9 LFDAYFTARDMREVFCDAGRVQAMLDVEAALARAEARVGLIPQSAVASIEKACRAEFYDFSTL 71 
                                                     7899*********************************************************** PP

                                       TIGR02426  64 aeaaaeagnvviplvkalrkavae...eaaryvHlGaTSQDviDTalmLqlrdaldllladle 123
                                                     +ea+a+agn++iplvkal k++a+   ea+ryvHlGaTSQDv+D +l+Lqlr+al l++ +l+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04910  72 SEAIASAGNSAIPLVKALGKRIAAedaEAERYVHLGATSQDVMDSGLVLQLRQALGLIEGELA 134
                                                     **********************9989999********************************** PP

                                       TIGR02426 124 rlaeaLaelaarhrdtpltarTllQqAvpttvglkaagwlaavlrardrlealrtealalqfG 186
                                                     +la++La++a+r + tpl +rT+lQ+A+p+t+g+k+agwl a++r+r+rl++l+ ++l+lqfG
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04910 135 QLAAILARQAERYATTPLAGRTWLQHATPVTLGMKIAGWLGAITRSRQRLKELKPRLLVLQFG 197
                                                     *************************************************************** PP

                                       TIGR02426 187 GAaGtlaalekkglavaealAaelgLeapalpWhtqrdriaelaaaLalvagalgkiaqDval 249
                                                     GA+Gtlaal++++l vaealAael+L++p++pWhtqrdr++e++a+L+l+ag+lgk+++D++l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04910 198 GASGTLAALGEHALPVAEALAAELQLTLPEQPWHTQRDRLVEFGAVLGLIAGSLGKLGRDISL 260
                                                     *************************************************************** PP

                                       TIGR02426 250 laqtevgevle.agg..GGSSampHKrNPvaaevlaaaarrapglvatLfaalaqedeRsagg 309
                                                     l+qte+ge++e +++  GGSS+mpHKrNPv+a+vl++aa+r+pgl++tLf+a++qe+eRs+g 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04910 261 LMQTEAGEAFEpSAPgkGGSSTMPHKRNPVGAAVLIGAATRVPGLLSTLFSAMPQEHERSLGL 323
                                                     ***********766689********************************************** PP

                                       TIGR02426 310 WhaeWetLrelvaltagalrqaaellegl 338
                                                     WhaeWetL+e+++l++gal+qa+ l+egl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04910 324 WHAEWETLPEICCLVSGALQQARLLAEGL 352
                                                     **************************997 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 14.07
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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