Alignments for a candidate for pcaB in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Pseudomonas simiae WCS417

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate GFF1324 PS417_06730 3-carboxy-cis,cis-muconate cycloisomerase

Query= uniprot:A0A0C4YE08
         (470 letters)



>FitnessBrowser__WCS417:GFF1324
          Length = 451

 Score =  457 bits (1175), Expect = e-133
 Identities = 240/447 (53%), Positives = 302/447 (67%), Gaps = 4/447 (0%)

Query: 3   TSSRLTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAG 62
           TS++L D  F + +    F D   +Q MLD EA LARA+A  GVIP  A   IA  C A 
Sbjct: 5   TSNQLFDAYFTAGSMAEVFCDQGRLQGMLDVEAGLARAQAQVGVIPQAAVAPIAQACLAS 64

Query: 63  EIDFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQLRE 122
             D DAL AA    GN AIPLV+ L   +A+ DA A RYVH GATSQD +DTG+VLQLR 
Sbjct: 65  LYDVDALGAAIATAGNSAIPLVKALGKLIASEDAGAERYVHLGATSQDVMDTGLVLQLRR 124

Query: 123 ALQAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRL 182
           A++ ++ADL  LG   AA A ++ D P+  RTWLQHA P T G+K AGWL A+ R+ +RL
Sbjct: 125 AVELIEADLVRLGDRLAAQAQRYADVPLAGRTWLQHATPVTLGMKIAGWLGAVTRNRQRL 184

Query: 183 DAARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVATTL 242
            A + +   LQFGGA+GTLA+LG  A  VA AL + L L++   PWH  RDR+VE A+ L
Sbjct: 185 TALKPRLLVLQFGGASGTLAALGEQAMPVAEALAAELQLSLPEQPWHTQRDRLVEFASVL 244

Query: 243 GMLTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRVPP 302
           G++ GSLGK+ RD+SL+MQTE AEV EP+ PG+GGSSTMPHKRNPVG A +++AA RVP 
Sbjct: 245 GLIAGSLGKLGRDISLLMQTEAAEVFEPSAPGKGGSSTMPHKRNPVGAAVLISAATRVPG 304

Query: 303 LVATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLG 362
           LV+TM + M QEHER+LG W AEW+TLP+I  L +GAL Q L V  GL+VD  RM  NL 
Sbjct: 305 LVSTMFSAMPQEHERSLGLWHAEWETLPEICRLVSGALHQALLVSEGLEVDPQRMAQNLD 364

Query: 363 VTHGLILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAGLM 422
           +THGL+LAEA  + L  ++GR  AHHL+E  C+RAVAEG  LR    A LA++      +
Sbjct: 365 LTHGLVLAEAVSIVLAQRLGRETAHHLLEQCCKRAVAEGRHLR----AVLADEPQVTAEL 420

Query: 423 DAAALDRVCDPANYAGQAAGFVDAVLA 449
            A  LDR+ DPA+Y GQA  +V   +A
Sbjct: 421 SAIELDRLLDPAHYLGQAHTWVTRAVA 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: 450
Number of extensions: 14
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: 451
Length adjustment: 33
Effective length of query: 437
Effective length of database: 418
Effective search space:   182666
Effective search space used:   182666
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 GFF1324 PS417_06730 (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.8414.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-141  457.1  12.2     2e-141  456.8  12.2    1.1  1  lcl|FitnessBrowser__WCS417:GFF1324  PS417_06730 3-carboxy-cis,cis-mu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1324  PS417_06730 3-carboxy-cis,cis-muconate cycloisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.8  12.2    2e-141    2e-141       1     338 []       9     352 ..       9     352 .. 0.98

  Alignments for each domain:
  == domain 1  score: 456.8 bits;  conditional E-value: 2e-141
                           TIGR02426   1 lldglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaaeagnvvi 75 
                                         l+d++f++  +ae+f d++rl++mldvEa laraqa+vG+ip++a++ ia a+ +  +D+ al +a+a+agn++i
  lcl|FitnessBrowser__WCS417:GFF1324   9 LFDAYFTAGSMAEVFCDQGRLQGMLDVEAGLARAQAQVGVIPQAAVAPIAQACLASLYDVDALGAAIATAGNSAI 83 
                                         78999********************************************************************** PP

                           TIGR02426  76 plvkalrkavae...eaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaelaarhrdtpltarTll 147
                                         plvkal k +a+    a+ryvHlGaTSQDv+DT+l+Lqlr+a++l++adl rl ++La++a+r +d pl +rT+l
  lcl|FitnessBrowser__WCS417:GFF1324  84 PLVKALGKLIASedaGAERYVHLGATSQDVMDTGLVLQLRRAVELIEADLVRLGDRLAAQAQRYADVPLAGRTWL 158
                                         ***********9777789********************************************************* PP

                           TIGR02426 148 QqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkglavaealAaelgLeapalpWhtq 222
                                         Q+A+p+t+g+k+agwl av+r+r+rl+al+ ++l+lqfGGA+Gtlaal+++++ vaealAael+L++p++pWhtq
  lcl|FitnessBrowser__WCS417:GFF1324 159 QHATPVTLGMKIAGWLGAVTRNRQRLTALKPRLLVLQFGGASGTLAALGEQAMPVAEALAAELQLSLPEQPWHTQ 233
                                         *************************************************************************** PP

                           TIGR02426 223 rdriaelaaaLalvagalgkiaqDvallaqtevgevle.agg..GGSSampHKrNPvaaevlaaaarrapglvat 294
                                         rdr++e+a++L+l+ag+lgk+++D++ll+qte++ev+e +++  GGSS+mpHKrNPv+a+vl++aa+r+pglv+t
  lcl|FitnessBrowser__WCS417:GFF1324 234 RDRLVEFASVLGLIAGSLGKLGRDISLLMQTEAAEVFEpSAPgkGGSSTMPHKRNPVGAAVLISAATRVPGLVST 308
                                         **************************************766689******************************* PP

                           TIGR02426 295 LfaalaqedeRsaggWhaeWetLrelvaltagalrqaaellegl 338
                                         +f+a++qe+eRs+g WhaeWetL+e+++l++gal+qa  ++egl
  lcl|FitnessBrowser__WCS417:GFF1324 309 MFSAMPQEHERSLGLWHAEWETLPEICRLVSGALHQALLVSEGL 352
                                         *************************************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (451 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: 8.71
//
[ok]

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

Downloads

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

Related tools

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