Alignments for a candidate for pcaB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Klebsiella michiganensis M5al

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate BWI76_RS16130 BWI76_RS16130 3-carboxy-cis,cis-muconate cycloisomerase

Query= uniprot:A0A0C4YE08
         (470 letters)



>FitnessBrowser__Koxy:BWI76_RS16130
          Length = 450

 Score =  451 bits (1159), Expect = e-131
 Identities = 242/448 (54%), Positives = 299/448 (66%), Gaps = 4/448 (0%)

Query: 7   LTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGEIDF 66
           L  PM  ++   A FSD   VQ MLDFEAALARA+  CG++P  A   I  TCR   IDF
Sbjct: 3   LLTPMMRTSPLTAWFSDAQRVQGMLDFEAALARAQVECGLVPQAALTPILETCRHENIDF 62

Query: 67  DALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQLREALQA 126
            AL  AA + GNLAIPLV+QLTARV  RD  AARY+HWGATSQDAIDTG +LQLR AL  
Sbjct: 63  AALGQAAASAGNLAIPLVKQLTARVRERDEAAARYLHWGATSQDAIDTGFILQLRGALAE 122

Query: 127 VDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRLDAAR 186
            ++ L+ L  A A+ A +++DT M  RTW+QHALP TFGLK AG LDAL R   RL   R
Sbjct: 123 TESLLQRLLDALASQAQRYQDTVMPGRTWMQHALPVTFGLKLAGTLDALLRWQTRLREMR 182

Query: 187 AQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVATTLGMLT 246
           ++   LQFGGAAGTL SL   AP VA AL   L L +  TPWH+ RDR++EV      + 
Sbjct: 183 SRVLALQFGGAAGTLDSLKTQAPQVAIALAKTLDLQLPDTPWHSQRDRLLEVGAWYAGVC 242

Query: 247 GSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRVPPLVAT 306
           G+LGK A D SL+MQ+EVAEVAEP   GRGGSSTMPHKRNP+ CAA+LTAA R P LVAT
Sbjct: 243 GTLGKFANDFSLLMQSEVAEVAEPVAEGRGGSSTMPHKRNPIACAAILTAAQRTPGLVAT 302

Query: 307 MLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLGVTHG 366
           +  G +Q+HERALGGWQAEW+TLP+++TL  GAL Q   +V  +QV   +MRA+L +THG
Sbjct: 303 LYTGQIQQHERALGGWQAEWETLPELMTLVGGALAQSEALVRDMQVFPPKMRADLEITHG 362

Query: 367 LILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAGLMDAAA 426
           LI+AEA  L L   IG+  AHH +E  CR+A+    +L+    + L  D   +  + A  
Sbjct: 363 LIMAEAVTLALAEFIGKADAHHRIEALCRQALDTSCSLQ----SVLENDPQVSEHLSADR 418

Query: 427 LDRVCDPANYAGQAAGFVDAVLAAWRHE 454
           L ++ DP    G AA FV  V+A ++ +
Sbjct: 419 LTQLLDPTTATGSAALFVRQVVARYKEQ 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: 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: 470
Length of database: 450
Length adjustment: 33
Effective length of query: 437
Effective length of database: 417
Effective search space:   182229
Effective search space used:   182229
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 BWI76_RS16130 BWI76_RS16130 (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.32045.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-126  407.7  14.1     3e-126  406.9  14.1    1.4  1  lcl|FitnessBrowser__Koxy:BWI76_RS16130  BWI76_RS16130 3-carboxy-cis,cis-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS16130  BWI76_RS16130 3-carboxy-cis,cis-muconate cycloisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.9  14.1    3e-126    3e-126       4     337 ..       6     345 ..       3     346 .. 0.97

  Alignments for each domain:
  == domain 1  score: 406.9 bits;  conditional E-value: 3e-126
                               TIGR02426   4 glfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaaeagnvv 74 
                                              ++ +s +++ fsd+ r+++mld+Eaalaraq+++Gl+p++a + i  ++++ ++D +al +aaa+agn++
  lcl|FitnessBrowser__Koxy:BWI76_RS16130   6 PMMRTSPLTAWFSDAQRVQGMLDFEAALARAQVECGLVPQAALTPILETCRHENIDFAALGQAAASAGNLA 76 
                                             55667889999************************************************************ PP

                               TIGR02426  75 iplvkalrkavae...eaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaelaarhrdtplt 142
                                             iplvk+l+++v e    aary+H+GaTSQD iDT+ +Lqlr al+  +  l+rl +aLa++a+r +dt ++
  lcl|FitnessBrowser__Koxy:BWI76_RS16130  77 IPLVKQLTARVRErdeAAARYLHWGATSQDAIDTGFILQLRGALAETESLLQRLLDALASQAQRYQDTVMP 147
                                             ***********99988899**************************************************** PP

                               TIGR02426 143 arTllQqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkglavaealAaelgLe 213
                                             +rT++Q+A+p+t+glk+ag l+a+lr ++rl+++r+++lalqfGGAaGtl +l++++ +va alA++l+L+
  lcl|FitnessBrowser__Koxy:BWI76_RS16130 148 GRTWMQHALPVTFGLKLAGTLDALLRWQTRLREMRSRVLALQFGGAAGTLDSLKTQAPQVAIALAKTLDLQ 218
                                             *********************************************************************** PP

                               TIGR02426 214 apalpWhtqrdriaelaaaLalvagalgkiaqDvallaqtevgevle..agg.GGSSampHKrNPvaaevl 281
                                             +p +pWh+qrdr+ e++a  a v+g+lgk+a+D +ll+q+ev+ev+e  a+g GGSS+mpHKrNP+a++++
  lcl|FitnessBrowser__Koxy:BWI76_RS16130 219 LPDTPWHSQRDRLLEVGAWYAGVCGTLGKFANDFSLLMQSEVAEVAEpvAEGrGGSSTMPHKRNPIACAAI 289
                                             ***********************************************754459****************** PP

                               TIGR02426 282 aaaarrapglvatLfaalaqedeRsaggWhaeWetLrelvaltagalrqaaelleg 337
                                             ++aa+r+pglvatL+    q++eR++ggW+aeWetL+el++l++gal+q ++l+ +
  lcl|FitnessBrowser__Koxy:BWI76_RS16130 290 LTAAQRTPGLVATLYTGQIQQHERALGGWQAEWETLPELMTLVGGALAQSEALVRD 345
                                             **************************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (450 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: 8.52
//
[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