Alignments for a candidate for pcaD in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaD in Herbaspirillum seropedicae SmR1

Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate HSERO_RS06525 HSERO_RS06525 3-oxoadipate enol-lactonase

Query= reanno::pseudo3_N2E3:AO353_17230
         (266 letters)



>FitnessBrowser__HerbieS:HSERO_RS06525
          Length = 261

 Score =  284 bits (726), Expect = 2e-81
 Identities = 140/253 (55%), Positives = 181/253 (71%), Gaps = 3/253 (1%)

Query: 11  LKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGRSLVTPGPYSI 70
           L YQL+G    PVLVLSNSLGT+L MWD Q+P + +HFRVLR+DTRGHG+S VTPG  SI
Sbjct: 11  LHYQLEGDASLPVLVLSNSLGTSLSMWDPQMPQWLQHFRVLRYDTRGHGQSEVTPGECSI 70

Query: 71  EQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNTAAKIGDPSVW 130
            QLG DV+ALLD L I +AHFCGLSMGG    WL ++  +R++KL++CNT AKIG    W
Sbjct: 71  AQLGSDVIALLDHLGIAQAHFCGLSMGGSTFMWLAVHHPQRINKLILCNTGAKIGTAEAW 130

Query: 131 NPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATSPQGYAANCAA 190
           N RIETV R+G   + A+  A ++RW TP++AQA+P   + +T ML AT  +GYAA CAA
Sbjct: 131 NSRIETVRREG---LGAIAGAVVSRWLTPEYAQAHPQQVQALTAMLLATPAEGYAAACAA 187

Query: 191 VRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYAAHLSNVQAGS 250
           VRD D RE +A I  PTL+IAG+ D  TPP+  +F++  + GA+Y EF AAH+SN Q  +
Sbjct: 188 VRDHDLREAIAGIRAPTLIIAGSGDVPTPPADAQFMRATIPGAQYVEFDAAHISNQQQAA 247

Query: 251 AFSDRVLSFLLAE 263
           AF+  V+ FL  +
Sbjct: 248 AFTQAVVQFLTGQ 260


Lambda     K      H
   0.321    0.136    0.410 

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: 238
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: 266
Length of database: 261
Length adjustment: 25
Effective length of query: 241
Effective length of database: 236
Effective search space:    56876
Effective search space used:    56876
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 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate HSERO_RS06525 HSERO_RS06525 (3-oxoadipate enol-lactonase)
to HMM TIGR02427 (pcaD: 3-oxoadipate enol-lactonase (EC 3.1.1.24))

# 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/TIGR02427.hmm
# target sequence database:        /tmp/gapView.431.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02427  [M=251]
Accession:   TIGR02427
Description: protocat_pcaD: 3-oxoadipate enol-lactonase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.1e-103  331.9   0.5   1.3e-103  331.8   0.5    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS06525  HSERO_RS06525 3-oxoadipate enol-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS06525  HSERO_RS06525 3-oxoadipate enol-lactonase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.8   0.5  1.3e-103  1.3e-103       1     251 []      10     258 ..      10     258 .. 0.99

  Alignments for each domain:
  == domain 1  score: 331.8 bits;  conditional E-value: 1.3e-103
                                  TIGR02427   1 rlhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladd 68 
                                                rlhy+leg++ + pvlvl+nSLGt+l++wd+++++  ++frvlryD+rGHG+S+v+ g+ si++l++d
  lcl|FitnessBrowser__HerbieS:HSERO_RS06525  10 RLHYQLEGDA-SLPVLVLSNSLGTSLSMWDPQMPQWLQHFRVLRYDTRGHGQSEVTPGECSIAQLGSD 76 
                                                69********.********************************************************* PP

                                  TIGR02427  69 vlallDalgiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeGlaa 136
                                                v+allD+lgi++a++cGlS+GG + ++La+++p+r+++l+l+nt akigtae W++Ri++vr+eGl a
  lcl|FitnessBrowser__HerbieS:HSERO_RS06525  77 VIALLDHLGIAQAHFCGLSMGGSTFMWLAVHHPQRINKLILCNTGAKIGTAEAWNSRIETVRREGLGA 144
                                                ******************************************************************** PP

                                  TIGR02427 137 ladavlerwFtpafreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeD 204
                                                +a av++rw tp++++a+p++++++++ml+++p+egYaa+caA+rd dlre++  i++Ptl+iaG+ D
  lcl|FitnessBrowser__HerbieS:HSERO_RS06525 145 IAGAVVSRWLTPEYAQAHPQQVQALTAMLLATPAEGYAAACAAVRDHDLREAIAGIRAPTLIIAGSGD 212
                                                ******************************************************************** PP

                                  TIGR02427 205 gstPpelvreiadlvpgarfaeieeaaHlpnleqpeafaallrdflk 251
                                                + tPp++++ + +++pga+++e++ aaH++n +q++af++++++fl+
  lcl|FitnessBrowser__HerbieS:HSERO_RS06525 213 VPTPPADAQFMRATIPGAQYVEFD-AAHISNQQQAAAFTQAVVQFLT 258
                                                ************************.********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (251 nodes)
Target sequences:                          1  (261 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: 5.57
//
[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