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.2203143.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.58
//
[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:

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:

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:

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:

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