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 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate HSERO_RS19935 HSERO_RS19935 hydrolase

Query= BRENDA::Q13KT2
         (263 letters)



>FitnessBrowser__HerbieS:HSERO_RS19935
          Length = 420

 Score =  154 bits (388), Expect = 4e-42
 Identities = 93/254 (36%), Positives = 126/254 (49%), Gaps = 5/254 (1%)

Query: 11  LHYRIDGERHGNAP--WIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGHGHSEAPKG 68
           LHY +   R+G AP   +VLS++LGTDL MW      L+   RV+ YD RGHG SE   G
Sbjct: 164 LHYTVREPRNGKAPRHTVVLSHALGTDLMMWDGLANQLAADCRVIAYDHRGHGSSEKADG 223

Query: 69  PYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALCNTAARI-- 126
            Y++  L  D   L+  L      + GLSMGG+ G  LA RH   +  + L NT +    
Sbjct: 224 LYSMADLADDAARLLRELDSGPVVWVGLSMGGMVGQELALRHPGLVRALVLANTTSAYPD 283

Query: 127 GSPEVWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDKEGYASN 186
            + E W  R    R EG+  +ADAV+ R+F   +   +   +A  R   V TD  GY   
Sbjct: 284 AAREAWQQRIATVRAEGIEVIADAVMGRYFHEGFRSAQAATVARYRQRLVTTDAVGYVGC 343

Query: 187 CEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARY-VELDASHISNI 245
           C A+   D       I+VP LVI+G  D     A  + L   I+GAR  V   ASH+S +
Sbjct: 344 CHAVGTVDTAARLGSIRVPTLVIAGELDQGTPVAMAQALVDGISGARLAVIAGASHVSAV 403

Query: 246 ERADAFTKTVVDFL 259
           E+   F + V  F+
Sbjct: 404 EQPALFAELVCGFI 417


Lambda     K      H
   0.320    0.134    0.402 

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: 293
Number of extensions: 18
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: 263
Length of database: 420
Length adjustment: 28
Effective length of query: 235
Effective length of database: 392
Effective search space:    92120
Effective search space used:    92120
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: 49 (23.5 bits)

Align candidate HSERO_RS19935 HSERO_RS19935 (hydrolase)
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.294841.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
    1.9e-81  259.1   2.1    2.5e-81  258.7   2.1    1.2  1  FitnessBrowser__HerbieS:HSERO_RS19935  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__HerbieS:HSERO_RS19935  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.7   2.1   2.5e-81   2.5e-81       2     250 ..     164     417 ..     163     418 .. 0.95

  Alignments for each domain:
  == domain 1  score: 258.7 bits;  conditional E-value: 2.5e-81
                              TIGR02427   2 lhyrlegaeadk...pvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvl 70 
                                            lhy+++ ++++k    ++vl+  LGtdl +wd  +++l++d rv++yD+rGHG+S+  +g ys++dladd +
  FitnessBrowser__HerbieS:HSERO_RS19935 164 LHYTVREPRNGKaprHTVVLSHALGTDLMMWDGLANQLAADCRVIAYDHRGHGSSEKADGLYSMADLADDAA 235
                                            89999877765422268******************************************************* PP

                              TIGR02427  71 allDalgiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigt..aesWeaRiaavraeGlaalada 140
                                            +ll +l+   ++ +GlS+GG+++q La+r+p +v+alvl+nt+    +  +e W++Ria+vraeG++++ada
  FitnessBrowser__HerbieS:HSERO_RS19935 236 RLLRELDSGPVVWVGLSMGGMVGQELALRHPGLVRALVLANTTSAYPDaaREAWQQRIATVRAEGIEVIADA 307
                                            *****************************************998886522699******************* PP

                              TIGR02427 141 vlerwFtpafreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpelv 212
                                            v+ r+F ++fr+a++a+++ +r+ lv++++ gY+++c+A+ ++d  +rl++i+vPtlviaG+ D+ tP + +
  FitnessBrowser__HerbieS:HSERO_RS19935 308 VMGRYFHEGFRSAQAATVARYRQRLVTTDAVGYVGCCHAVGTVDTAARLGSIRVPTLVIAGELDQGTPVAMA 379
                                            ************************************************************************ PP

                              TIGR02427 213 reiadlvpgarfaeieeaaHlpnleqpeafaallrdfl 250
                                            ++++d ++gar+a+i++a+H++++eqp+ fa+l+ +f+
  FitnessBrowser__HerbieS:HSERO_RS19935 380 QALVDGISGARLAVIAGASHVSAVEQPALFAELVCGFI 417
                                            **********************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (251 nodes)
Target sequences:                          1  (420 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: 17.81
//
[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