Alignments for a candidate for pcaB in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Pseudomonas putida KT2440

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate PP_1379 PP_1379 3-carboxy-cis,cis-muconate cycloisomerase

Query= uniprot:A0A0C4YE08
         (470 letters)



>FitnessBrowser__Putida:PP_1379
          Length = 450

 Score =  443 bits (1140), Expect = e-129
 Identities = 236/441 (53%), Positives = 295/441 (66%), Gaps = 4/441 (0%)

Query: 4   SSRLTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGE 63
           S++L D  F + A    FSD   +Q MLDFEAALARAEAS G++P  A  AI A C+A  
Sbjct: 2   SNQLFDAYFTAPAMREIFSDRGRLQGMLDFEAALARAEASAGLVPHSAVAAIEAACQAER 61

Query: 64  IDFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQLREA 123
            D  ALA A    GN AIPLV+ L   +A    +A RYVH GATSQDA+DTG+VLQLR+A
Sbjct: 62  YDVGALANAIATAGNSAIPLVKALGKVIATGVPEAERYVHLGATSQDAMDTGLVLQLRDA 121

Query: 124 LQAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRLD 183
           L  ++ADL  L    +  A +H DTP+V RTWLQHA P T G+K AG L AL R  +RL 
Sbjct: 122 LDLIEADLGKLADTLSQQALKHADTPLVGRTWLQHATPVTLGMKLAGVLGALTRHRQRLQ 181

Query: 184 AARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVATTLG 243
             R +   LQFGGA+G+LA+LG+ A  VA AL   L L +   PWH  RDR+VE A+ LG
Sbjct: 182 ELRPRLLVLQFGGASGSLAALGSKAMPVAEALAEQLKLTLPEQPWHTQRDRLVEFASVLG 241

Query: 244 MLTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRVPPL 303
           ++ GSLGK  RD+SL+MQTE  EV EP+ PG+GGSSTMPHKRNPVG A ++ AA RVP L
Sbjct: 242 LVAGSLGKFGRDISLLMQTEAGEVFEPSAPGKGGSSTMPHKRNPVGAAVLIGAATRVPGL 301

Query: 304 VATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLGV 363
           ++T+ A M QEHER+LG W AEW+TLP I  L +GALRQ   +  G++VDAARMR NL +
Sbjct: 302 LSTLFAAMPQEHERSLGLWHAEWETLPDICCLVSGALRQAQVIAEGMEVDAARMRRNLDL 361

Query: 364 THGLILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAGLMD 423
           T GL+LAEA  + L  ++GR  AHHL+E  C+RAVAE   LR  LG    ++   +  + 
Sbjct: 362 TQGLVLAEAVSIVLAQRLGRDRAHHLLEQCCQRAVAEQRHLRAVLG----DEPQVSAELS 417

Query: 424 AAALDRVCDPANYAGQAAGFV 444
              LDR+ DPA+Y GQA  +V
Sbjct: 418 GEELDRLLDPAHYLGQARVWV 438


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: 476
Number of extensions: 12
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: 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 PP_1379 PP_1379 (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.25753.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.3e-152  493.5   9.8   1.7e-152  493.2   9.8    1.1  1  lcl|FitnessBrowser__Putida:PP_1379  PP_1379 3-carboxy-cis,cis-mucona


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1379  PP_1379 3-carboxy-cis,cis-muconate cycloisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  493.2   9.8  1.7e-152  1.7e-152       1     338 []       5     348 ..       5     348 .. 0.99

  Alignments for each domain:
  == domain 1  score: 493.2 bits;  conditional E-value: 1.7e-152
                           TIGR02426   1 lldglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaaeagnvvi 75 
                                         l+d++f++++++e+fsdr+rl++mld+Eaalara+a++Gl+p++a++ai+aa+++ ++D+ ala+a+a+agn++i
  lcl|FitnessBrowser__Putida:PP_1379   5 LFDAYFTAPAMREIFSDRGRLQGMLDFEAALARAEASAGLVPHSAVAAIEAACQAERYDVGALANAIATAGNSAI 79 
                                         7899*********************************************************************** PP

                           TIGR02426  76 plvkalrkavae...eaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaelaarhrdtpltarTll 147
                                         plvkal k++a+   ea+ryvHlGaTSQD +DT+l+Lqlrdaldl++adl++la++L+++a +h+dtpl++rT+l
  lcl|FitnessBrowser__Putida:PP_1379  80 PLVKALGKVIATgvpEAERYVHLGATSQDAMDTGLVLQLRDALDLIEADLGKLADTLSQQALKHADTPLVGRTWL 154
                                         ************9************************************************************** PP

                           TIGR02426 148 QqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkglavaealAaelgLeapalpWhtq 222
                                         Q+A+p+t+g+k+ag+l a++r+r+rl++lr ++l+lqfGGA+G+laal++k++ vaealA++l+L++p++pWhtq
  lcl|FitnessBrowser__Putida:PP_1379 155 QHATPVTLGMKLAGVLGALTRHRQRLQELRPRLLVLQFGGASGSLAALGSKAMPVAEALAEQLKLTLPEQPWHTQ 229
                                         *************************************************************************** PP

                           TIGR02426 223 rdriaelaaaLalvagalgkiaqDvallaqtevgevle.agg..GGSSampHKrNPvaaevlaaaarrapglvat 294
                                         rdr++e+a++L+lvag+lgk+++D++ll+qte+gev+e +++  GGSS+mpHKrNPv+a+vl++aa+r+pgl++t
  lcl|FitnessBrowser__Putida:PP_1379 230 RDRLVEFASVLGLVAGSLGKFGRDISLLMQTEAGEVFEpSAPgkGGSSTMPHKRNPVGAAVLIGAATRVPGLLST 304
                                         **************************************766689******************************* PP

                           TIGR02426 295 LfaalaqedeRsaggWhaeWetLrelvaltagalrqaaellegl 338
                                         Lfaa++qe+eRs+g WhaeWetL+++++l++galrqa++++eg+
  lcl|FitnessBrowser__Putida:PP_1379 305 LFAAMPQEHERSLGLWHAEWETLPDICCLVSGALRQAQVIAEGM 348
                                         *****************************************997 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: 11.09
//
[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