Aligments for a candidate for pcaB in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments for a candidate for pcaB in Sinorhizobium meliloti 1021

Align 3-Carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2) (characterized)
to candidate SM_b20575 SM_b20575 3-carboxy-cis,cis-muconate cycloisomerase

Query= BRENDA::Q2HNZ1
         (353 letters)



>FitnessBrowser__Smeli:SM_b20575
          Length = 351

 Score =  392 bits (1006), Expect = e-113
 Identities = 206/349 (59%), Positives = 247/349 (70%)

Query: 1   MSLSPFEHPFLSGLFGDSEIIELFSAKADIDAMIRFETALAQAEAEASIFADDEAEAIVS 60
           M+ S F+HP+LSGL GD  +   FS  AD+ AM+ FE ALA+AEA   +  +  A  I  
Sbjct: 1   MTYSAFDHPYLSGLLGDEAVAAEFSVVADVRAMLAFEAALARAEARHGVIPEAAANRIAE 60

Query: 61  GLSEFAADMSALRHGVAKDGVVVPELIRQMRAAVAGQGADKVHFGATSQDVIDTSLMLRL 120
               F+ D+ A+R   A DGVVVPEL+RQ+R AV  + A+ VHFGATSQDV+DTSLMLRL
Sbjct: 61  ACRGFSPDVGAMRRATAIDGVVVPELVRQLRRAVGEEAAEHVHFGATSQDVVDTSLMLRL 120

Query: 121 KMAAEIIATRLGHLIDTLGDLASRDGHKPLTGYTRMQAAIGITVADRAAGWIAPLERHLL 180
           K  AE+ + R+G ++  L       G + LT +TRMQ AI ITVADR   WI PL  H  
Sbjct: 121 KAIAELFSGRVGDVVTALEACGRHWGERALTAHTRMQPAIAITVADRLRSWIEPLLDHQD 180

Query: 181 RLETFAQNGFALQFGGAAGTLEKLGDNAGAVRADLAKRLGLADRPQWHNQRDGIPEFANL 240
           RL+T   + FA+QFGGAAGTLEKL   A  VRA LA+ L L D PQWH+QR  I +FA+L
Sbjct: 181 RLDTTGTDIFAVQFGGAAGTLEKLKGKADIVRATLAEELALVDCPQWHSQRLPIADFAHL 240

Query: 241 LSLVTGTLGKFGQDIALMAEIGSEIRLSGGGGSSAMPHKQNPVNAETLVTLARFNAVQIS 300
           LSLVTG+LGKFGQD+ALMA+ G EI L+GGGGSSAMPHKQNPV AE LVTLARFNA Q+S
Sbjct: 241 LSLVTGSLGKFGQDVALMAQAGDEIVLAGGGGSSAMPHKQNPVAAEVLVTLARFNATQVS 300

Query: 301 ALHQSLVQEQERSGAGWMLEWLTLPQMVTATGTSLLVAERLAAQIDRLG 349
           A+HQSLV EQERSG+ W LEWL LPQMV AT  +L +A  LA  + RLG
Sbjct: 301 AIHQSLVHEQERSGSAWTLEWLILPQMVGATAAALRLAAELAGNVRRLG 349


Lambda     K      H
   0.318    0.133    0.376 

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: 401
Number of extensions: 17
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: 353
Length of database: 351
Length adjustment: 29
Effective length of query: 324
Effective length of database: 322
Effective search space:   104328
Effective search space used:   104328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate SM_b20575 SM_b20575 (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.17412.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   7.2e-123  395.7  16.9   8.1e-123  395.6  16.9    1.0  1  lcl|FitnessBrowser__Smeli:SM_b20575  SM_b20575 3-carboxy-cis,cis-muco


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b20575  SM_b20575 3-carboxy-cis,cis-muconate cycloisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.6  16.9  8.1e-123  8.1e-123       2     336 ..      11     343 ..      10     345 .. 0.99

  Alignments for each domain:
  == domain 1  score: 395.6 bits;  conditional E-value: 8.1e-123
                            TIGR02426   2 ldglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaaeagnvvi 75 
                                          l+gl gd+++a+ fs  a++raml++Eaalara+a+ G+ip++aa++ia a++ +++D+ a+++a+a +g+vv+
  lcl|FitnessBrowser__Smeli:SM_b20575  11 LSGLLGDEAVAAEFSVVADVRAMLAFEAALARAEARHGVIPEAAANRIAEACRGFSPDVGAMRRATAIDGVVVP 84 
                                          68999********************************************************************* PP

                            TIGR02426  76 plvkalrkavaeeaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaelaarhrdtpltarTllQq 149
                                          +lv++lr+av+eeaa++vH+GaTSQDv+DT+lmL+l++ ++l   +++ ++ aL +  ++ ++ +lta+T++Q+
  lcl|FitnessBrowser__Smeli:SM_b20575  85 ELVRQLRRAVGEEAAEHVHFGATSQDVVDTSLMLRLKAIAELFSGRVGDVVTALEACGRHWGERALTAHTRMQP 158
                                          ************************************************************************** PP

                            TIGR02426 150 AvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkglavaealAaelgLeapalpWhtqr 223
                                          A+++tv++++ +w++++l+++drl++  t+++a+qfGGAaGtl++l+ k+  v++ lA+el L +   +Wh+qr
  lcl|FitnessBrowser__Smeli:SM_b20575 159 AIAITVADRLRSWIEPLLDHQDRLDTTGTDIFAVQFGGAAGTLEKLKGKADIVRATLAEELALVD-CPQWHSQR 231
                                          *****************************************************************.9******* PP

                            TIGR02426 224 driaelaaaLalvagalgkiaqDvallaqtevgevleaggGGSSampHKrNPvaaevlaaaarrapglvatLfa 297
                                           +ia++a++L+lv+g+lgk++qDval+aq+  ++vl  ggGGSSampHK+NPvaaevl+++ar+++++v+++++
  lcl|FitnessBrowser__Smeli:SM_b20575 232 LPIADFAHLLSLVTGSLGKFGQDVALMAQAGDEIVLA-GGGGSSAMPHKQNPVAAEVLVTLARFNATQVSAIHQ 304
                                          **********************************998.99********************************** PP

                            TIGR02426 298 alaqedeRsaggWhaeWetLrelvaltagalrqaaelle 336
                                          +l++e+eRs+++W +eW +L+++v +ta+alr aael+ 
  lcl|FitnessBrowser__Smeli:SM_b20575 305 SLVHEQERSGSAWTLEWLILPQMVGATAAALRLAAELAG 343
                                          *********************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (351 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 6.70
//
[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, or view the source code.

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