Alignments for a candidate for pcaB in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Caulobacter crescentus NA1000

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate CCNA_02493 CCNA_02493 3-carboxy-cis,cis-muconate cycloisomerase

Query= uniprot:A0A0C4YE08
         (470 letters)



>FitnessBrowser__Caulo:CCNA_02493
          Length = 382

 Score =  305 bits (782), Expect = 1e-87
 Identities = 181/373 (48%), Positives = 223/373 (59%), Gaps = 5/373 (1%)

Query: 4   SSRLTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGE 63
           S  L D    +   L AFSD A ++  L FE  LARA+A  G+IP+DAAE IA  C A  
Sbjct: 2   SCLLRDRPASTPEMLTAFSDEALLRAALTFETMLARAQADVGLIPSDAAETIAIAC-AEL 60

Query: 64  IDFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQLREA 123
            D  +LA AA   G LAIPLV  +  R+A  D + A+ VH GATSQD  DT ++LQ +  
Sbjct: 61  PDVVSLAEAAAHAGTLAIPLVALIRERIA--DPEVAKLVHKGATSQDLADTALMLQAKTG 118

Query: 124 LQAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRLD 183
              V  D   L  A A LA +H  TPM+ RT LQ A P TFGLKAAGWL  +   L R +
Sbjct: 119 AALVLRDASRLAQALAVLAQRHAATPMLGRTLLQAAQPITFGLKAAGWLQGVASALARFE 178

Query: 184 AARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVATTLG 243
                A  +Q GGA G+LA L   A  VA  L + L L    TPWHA R+ +  +A++L 
Sbjct: 179 RETG-AIQMQLGGATGSLAGLDGRAGDVAERLAARLGLPAPETPWHARREGLAGLASSLA 237

Query: 244 MLTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRVPPL 303
           +LTG++GKIA D++LM QTEVAE  EP   GRGGSSTM HKRNP GC   L+A++R P L
Sbjct: 238 ILTGAVGKIAGDIALMAQTEVAEAFEPKVVGRGGSSTMAHKRNPTGCQVALSASIRAPHL 297

Query: 304 VATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLGV 363
            AT+L+ + Q+HER LGGWQ E   L ++  LA GAL  M  VV GL+VDA RM  NL  
Sbjct: 298 AATILSALPQQHERGLGGWQVEGPVLAELFELAHGALAAMAIVVEGLEVDADRMAVNLAA 357

Query: 364 TH-GLILAEAAML 375
              G  + EA  L
Sbjct: 358 ARVGSDIGEAERL 370


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: 369
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 470
Length of database: 382
Length adjustment: 32
Effective length of query: 438
Effective length of database: 350
Effective search space:   153300
Effective search space used:   153300
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 CCNA_02493 CCNA_02493 (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.9806.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-134  434.5  24.3   1.4e-134  434.2  24.3    1.1  1  lcl|FitnessBrowser__Caulo:CCNA_02493  CCNA_02493 3-carboxy-cis,cis-muc


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02493  CCNA_02493 3-carboxy-cis,cis-muconate cycloisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.2  24.3  1.4e-134  1.4e-134       1     338 []       5     344 ..       5     344 .. 0.98

  Alignments for each domain:
  == domain 1  score: 434.2 bits;  conditional E-value: 1.4e-134
                             TIGR02426   1 lldglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaaeagnv 73 
                                           l d+ ++++e+ ++fsd+a lra+l++E++laraqadvGlip++aae+ia+a+ael  D+ +laeaaa+ag++
  lcl|FitnessBrowser__Caulo:CCNA_02493   5 LRDRPASTPEMLTAFSDEALLRAALTFETMLARAQADVGLIPSDAAETIAIACAELP-DVVSLAEAAAHAGTL 76 
                                           678999************************************************776.*************** PP

                             TIGR02426  74 viplvkalrkavae.eaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaelaarhrdtpltarT 145
                                           +iplv+ +r+++a+ e+a++vH+GaTSQD+ DTalmLq++++++l+l+d +rla+aLa la+rh++tp+++rT
  lcl|FitnessBrowser__Caulo:CCNA_02493  77 AIPLVALIRERIADpEVAKLVHKGATSQDLADTALMLQAKTGAALVLRDASRLAQALAVLAQRHAATPMLGRT 149
                                           ************************************************************************* PP

                             TIGR02426 146 llQqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkglavaealAaelgLeapalp 218
                                           llQ+A+p+t+glkaagwl++v++a +r+e+ +t a+++q+GGA+G+la l+ ++ +vae+lAa+lgL+ap++p
  lcl|FitnessBrowser__Caulo:CCNA_02493 150 LLQAAQPITFGLKAAGWLQGVASALARFER-ETGAIQMQLGGATGSLAGLDGRAGDVAERLAARLGLPAPETP 221
                                           ******************************.779*************************************** PP

                             TIGR02426 219 WhtqrdriaelaaaLalvagalgkiaqDvallaqtevgevle.agg..GGSSampHKrNPvaaevlaaaarra 288
                                           Wh++r+++a la++La+++ga+gkia+D+al+aqtev+e++e +++  GGSS+m+HKrNP++++v+++a++ra
  lcl|FitnessBrowser__Caulo:CCNA_02493 222 WHARREGLAGLASSLAILTGAVGKIAGDIALMAQTEVAEAFEpKVVgrGGSSTMAHKRNPTGCQVALSASIRA 294
                                           ******************************************765579************************* PP

                             TIGR02426 289 pglvatLfaalaqedeRsaggWhaeWetLrelvaltagalrqaaellegl 338
                                           p+l+at+++al+q++eR++ggW++e+ +L+el++l++gal+++a ++egl
  lcl|FitnessBrowser__Caulo:CCNA_02493 295 PHLAATILSALPQQHERGLGGWQVEGPVLAELFELAHGALAAMAIVVEGL 344
                                           ************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (382 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: 12.88
//
[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