Alignments for a candidate for pcaB in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Herbaspirillum seropedicae SmR1

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate HSERO_RS19930 HSERO_RS19930 3-carboxy-cis,cis-muconate cycloisomerase

Query= uniprot:A0A0C4YE08
         (470 letters)



>FitnessBrowser__HerbieS:HSERO_RS19930
          Length = 455

 Score =  349 bits (896), Expect = e-100
 Identities = 198/430 (46%), Positives = 248/430 (57%)

Query: 4   SSRLTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGE 63
           S  + D    ++  +A F D A VQ ML FE  LA A+A+ GVIP  AA AIA+ CRA  
Sbjct: 2   SVSIFDSFLTTSEMIAVFDDQAVVQAMLRFEQVLAEAQAAEGVIPDAAARAIASVCRAPL 61

Query: 64  IDFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQLREA 123
            D  AL  A    G LAIPLV++L   VA    +AA +VHWG+TSQD +DT MVL  REA
Sbjct: 62  YDIPALIVAGRRAGALAIPLVKELQRTVALYSEEAATHVHWGSTSQDVLDTAMVLVTREA 121

Query: 124 LQAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRLD 183
           L+ V+ +L+ L      LA  H DTP++ART +Q A  T+ GLK   W   L R   +L 
Sbjct: 122 LRLVEGELEQLSRRLLDLAQSHLDTPVLARTLMQPAQVTSLGLKFCNWAAPLLRSRAQLQ 181

Query: 184 AARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVATTLG 243
           A   +A  LQ GGA GTL  LG   PAVA  + +AL L      WH  RD+ + +   + 
Sbjct: 182 ALAERALQLQLGGAVGTLTVLGEKGPAVAARMAAALELKTPEAAWHTQRDQWIRLGAEMA 241

Query: 244 MLTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRVPPL 303
           +L GSLGKIA D+SLM Q E+AE+AEP+G GRGGSS MPHKRNPV     L AA R P  
Sbjct: 242 VLAGSLGKIATDLSLMAQGEIAELAEPSGNGRGGSSAMPHKRNPVSSMIALAAAARAPQQ 301

Query: 304 VATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLGV 363
            A +LA M Q+HER LG WQAE    P +     GALR + +   GL +DA RM  N+  
Sbjct: 302 AAALLAAMSQQHERGLGNWQAELAEWPALFLGVHGALRALNDAFAGLVIDAPRMLRNIDA 361

Query: 364 THGLILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAGLMD 423
             GL+ AE+A + L G IGR  AH L+E   R+AVA+G  L   L   +  DA     +D
Sbjct: 362 LQGLVFAESASIALAGVIGRPRAHSLLEQLTRKAVADGAQLVDVLVDAVQADAQLRKEID 421

Query: 424 AAALDRVCDP 433
              L  + DP
Sbjct: 422 LPMLRGLFDP 431


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: 376
Number of extensions: 16
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: 455
Length adjustment: 33
Effective length of query: 437
Effective length of database: 422
Effective search space:   184414
Effective search space used:   184414
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 HSERO_RS19930 HSERO_RS19930 (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.16904.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   7.3e-115  369.4  22.0   1.2e-114  368.7  22.0    1.3  1  lcl|FitnessBrowser__HerbieS:HSERO_RS19930  HSERO_RS19930 3-carboxy-cis,cis-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS19930  HSERO_RS19930 3-carboxy-cis,cis-muconate cycloisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  368.7  22.0  1.2e-114  1.2e-114       3     338 .]       7     348 ..       5     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 368.7 bits;  conditional E-value: 1.2e-114
                                  TIGR02426   3 dglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaaea 70 
                                                d + ++se+ ++f+d+a ++aml++E +la+aqa+ G+ip++aa+aia+++++  +D+ al  a ++a
  lcl|FitnessBrowser__HerbieS:HSERO_RS19930   7 DSFLTTSEMIAVFDDQAVVQAMLRFEQVLAEAQAAEGVIPDAAARAIASVCRAPLYDIPALIVAGRRA 74 
                                                677899************************************************************** PP

                                  TIGR02426  71 gnvviplvkalrkavae...eaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaelaar 135
                                                g ++iplvk+l+++va    eaa +vH+G TSQDv+DTa++L+ r+al l++ +le+l+++L +la++
  lcl|FitnessBrowser__HerbieS:HSERO_RS19930  75 GALAIPLVKELQRTVALyseEAATHVHWGSTSQDVLDTAMVLVTREALRLVEGELEQLSRRLLDLAQS 142
                                                ***************97778************************************************ PP

                                  TIGR02426 136 hrdtpltarTllQqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkglava 203
                                                h dtp++arTl+Q+A+ t +glk+ +w a++lr+r++l+al+++al+lq+GGA+Gtl+ l++kg ava
  lcl|FitnessBrowser__HerbieS:HSERO_RS19930 143 HLDTPVLARTLMQPAQVTSLGLKFCNWAAPLLRSRAQLQALAERALQLQLGGAVGTLTVLGEKGPAVA 210
                                                ******************************************************************** PP

                                  TIGR02426 204 ealAaelgLeapalpWhtqrdriaelaaaLalvagalgkiaqDvallaqtevgevle.agg...GGSS 267
                                                +++Aa+l+L++p++ Whtqrd+  +l+a +a++ag+lgkia+D++l+aq e++e++e + g   GGSS
  lcl|FitnessBrowser__HerbieS:HSERO_RS19930 211 ARMAAALELKTPEAAWHTQRDQWIRLGAEMAVLAGSLGKIATDLSLMAQGEIAELAEpS-GngrGGSS 277
                                                *********************************************************64.3479**** PP

                                  TIGR02426 268 ampHKrNPvaaevlaaaarrapglvatLfaalaqedeRsaggWhaeWetLrelvaltagalrqaaell 335
                                                ampHKrNPv +++++aaa+rap+++a+L+aa+ q++eR++g+W+ae +  + l+  ++galr+ ++  
  lcl|FitnessBrowser__HerbieS:HSERO_RS19930 278 AMPHKRNPVSSMIALAAAARAPQQAAALLAAMSQQHERGLGNWQAELAEWPALFLGVHGALRALNDAF 345
                                                ***************************************************************99988 PP

                                  TIGR02426 336 egl 338
                                                +gl
  lcl|FitnessBrowser__HerbieS:HSERO_RS19930 346 AGL 348
                                                886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (455 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: 8.42
//
[ok]

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

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Candidates (tab-delimited)
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Protein sequences (fasta format)
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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