Alignments for a candidate for pcaB in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Paraburkholderia bryophila 376MFSha3.1

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate H281DRAFT_01595 H281DRAFT_01595 3-carboxy-cis,cis-muconate cycloisomerase

Query= uniprot:A0A0C4YE08
         (470 letters)



>FitnessBrowser__Burk376:H281DRAFT_01595
          Length = 459

 Score =  503 bits (1294), Expect = e-147
 Identities = 271/449 (60%), Positives = 311/449 (69%), Gaps = 4/449 (0%)

Query: 1   MPTSSRLTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCR 60
           + +S RLT  + G+      +S  AT+QRMLD EAALARA A+  VIP  A  AI A C 
Sbjct: 2   LDSSGRLTGLLCGTQPMNDIWSPRATLQRMLDVEAALARASAAHHVIPETAVPAIEAACH 61

Query: 61  AGEIDFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQL 120
           A ++D DALA  A  GGNLAIPLV+QLTARV A DA+A++YVHWGATSQD IDT  VLQL
Sbjct: 62  ADQLDADALARDAALGGNLAIPLVKQLTARVKAADAEASKYVHWGATSQDIIDTATVLQL 121

Query: 121 REALQAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLR 180
           RE    +D+ L+A   A A LAA HR TPM+ RTWLQ ALP T GLK A WLDAL R   
Sbjct: 122 RETFNLLDSGLQATCDAIAKLAATHRATPMIGRTWLQQALPITLGLKFAQWLDALLRHRE 181

Query: 181 RLDAARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVAT 240
           RLDA RA+A  LQFGGAAGTLASL  AAP V  AL   L L V   PWH  RDR+ E A+
Sbjct: 182 RLDALRARALVLQFGGAAGTLASLRDAAPQVTQALAQELGLTVPTLPWHTQRDRIAESAS 241

Query: 241 TLGMLTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRV 300
             GML G+LGKIARD+SL MQTE+ E+AEP   G+GGSSTMPHKRNPVGCAAVLTAA R 
Sbjct: 242 FFGMLIGTLGKIARDISLQMQTEIDELAEPAASGKGGSSTMPHKRNPVGCAAVLTAATRA 301

Query: 301 PPLVATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRAN 360
           P LVAT+ AGMVQEHERALGGWQAEWD LP +  LA GAL  + ++  GL V+  R+ AN
Sbjct: 302 PGLVATVFAGMVQEHERALGGWQAEWDALPDLARLAGGALANIEQIATGLNVNVPRLAAN 361

Query: 361 LGVTHGLILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAG 420
           L VTHGLIL EA ML LG  IGR+ AHHLVE A + A+ +G TL   L A    DAA   
Sbjct: 362 LDVTHGLILGEAVMLALGDSIGRMDAHHLVERASKAAIRDGQTLFDVLSA----DAAVTQ 417

Query: 421 LMDAAALDRVCDPANYAGQAAGFVDAVLA 449
            +    L ++ DPA Y GQA  +VDA LA
Sbjct: 418 HLSVERLKQLLDPAQYVGQAHAYVDAALA 446


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: 497
Number of extensions: 19
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: 459
Length adjustment: 33
Effective length of query: 437
Effective length of database: 426
Effective search space:   186162
Effective search space used:   186162
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 H281DRAFT_01595 H281DRAFT_01595 (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.10417.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.6e-133  430.8  20.6   2.3e-133  430.3  20.6    1.2  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01595  H281DRAFT_01595 3-carboxy-cis,ci


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01595  H281DRAFT_01595 3-carboxy-cis,cis-muconate cycloisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.3  20.6  2.3e-133  2.3e-133       5     338 .]      12     351 ..       8     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 430.3 bits;  conditional E-value: 2.3e-133
                                    TIGR02426   5 lfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaaea 70 
                                                  l g++ +++++s ra+l+ mldvEaalara a+  +ip+ a+ ai+aa+++ +lD  ala+ aa +
  lcl|FitnessBrowser__Burk376:H281DRAFT_01595  12 LCGTQPMNDIWSPRATLQRMLDVEAALARASAAHHVIPETAVPAIEAACHADQLDADALARDAALG 77 
                                                  678999************************************************************ PP

                                    TIGR02426  71 gnvviplvkalrkavae...eaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaela 133
                                                  gn++iplvk+l+++v +   ea +yvH+GaTSQD+iDTa++Lqlr++++ll+  l+++++a+a+la
  lcl|FitnessBrowser__Burk376:H281DRAFT_01595  78 GNLAIPLVKQLTARVKAadaEASKYVHWGATSQDIIDTATVLQLRETFNLLDSGLQATCDAIAKLA 143
                                                  *************997667999******************************************** PP

                                    TIGR02426 134 arhrdtpltarTllQqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkg 199
                                                  a+hr+tp+++rT+lQqA+p+t+glk+a wl+a+lr+r+rl+alr++al+lqfGGAaGtla+l  ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01595 144 ATHRATPMIGRTWLQQALPITLGLKFAQWLDALLRHRERLDALRARALVLQFGGAAGTLASLRDAA 209
                                                  ****************************************************************** PP

                                    TIGR02426 200 lavaealAaelgLeapalpWhtqrdriaelaaaLalvagalgkiaqDvallaqtevgevle.agg. 263
                                                   +v +alA+elgL+ p+lpWhtqrdriae a+ ++++ g+lgkia+D++l +qte++e++e a++ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_01595 210 PQVTQALAQELGLTVPTLPWHTQRDRIAESASFFGMLIGTLGKIARDISLQMQTEIDELAEpAASg 275
                                                  *************************************************************84445 PP

                                    TIGR02426 264 .GGSSampHKrNPvaaevlaaaarrapglvatLfaalaqedeRsaggWhaeWetLrelvaltagal 328
                                                   GGSS+mpHKrNPv+++++++aa+rapglvat+fa ++qe+eR++ggW+aeW +L++l++l++gal
  lcl|FitnessBrowser__Burk376:H281DRAFT_01595 276 kGGSSTMPHKRNPVGCAAVLTAATRAPGLVATVFAGMVQEHERALGGWQAEWDALPDLARLAGGAL 341
                                                  9***************************************************************** PP

                                    TIGR02426 329 rqaaellegl 338
                                                  ++++++++gl
  lcl|FitnessBrowser__Burk376:H281DRAFT_01595 342 ANIEQIATGL 351
                                                  ******9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (459 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: 9.46
//
[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