Alignments for a candidate for ech in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Herbaspirillum seropedicae SmR1

Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized)
to candidate HSERO_RS20640 HSERO_RS20640 enoyl-CoA hydratase

Query= curated2:P24162
         (257 letters)



>FitnessBrowser__HerbieS:HSERO_RS20640
          Length = 263

 Score =  246 bits (627), Expect = 5e-70
 Identities = 131/263 (49%), Positives = 176/263 (66%), Gaps = 6/263 (2%)

Query: 1   MSYHTIRYEISEGLAVITLDRPEVMNALNAAMRHELTAALHRARGE--ARAIVLTGSGRA 58
           MS  +I  E  +G+AVITL+RP+ +N+   AM  EL  A+   + +   R ++LTG+GR 
Sbjct: 1   MSSPSILLENRDGIAVITLNRPDKLNSFTVAMHLELRDAIATLQADPSVRVLLLTGAGRG 60

Query: 59  FCSGQDLGDGAA----EGLNLETVLREEYEPLLQAIYSCPLPVLAAVNGAAAGAGANLAL 114
           FC+GQDLGD A     +G++L   + + Y PL++++ + P PV+ AVNG AAGAGANL L
Sbjct: 61  FCAGQDLGDRAVKPGDDGVDLGESIDKYYGPLVKSLRALPFPVICAVNGVAAGAGANLPL 120

Query: 115 AADVVIAAQSAAFMQAFTRIGLMPDAGGTWWLPRQVGMARAMGMALFAEKIGAEEAARMG 174
           A D+V+AA+SA+F++ F ++GL+PD GGT++LPR VG ARAMGMAL  EKI AE+A R G
Sbjct: 121 ACDIVLAARSASFVEVFCKLGLIPDTGGTYFLPRLVGTARAMGMALLGEKISAEQAERWG 180

Query: 175 LIWEAVPDVDFEHHWRARAAHLARGPSAAFAAVKKAFHAGLSNPLPAQLALEARLQGELG 234
           LIW+ V D        A AAH AR P+   AA K   +A  ++ LP QL LE      LG
Sbjct: 181 LIWKCVDDDQLMEEAHAMAAHFARAPTKGLAATKATLYASPAHTLPEQLDLERDTMRALG 240

Query: 235 QSADFREGVQAFLEKRPPHFTGR 257
           +S D+REGV AFLEKR P FTG+
Sbjct: 241 RSRDYREGVTAFLEKRAPQFTGQ 263


Lambda     K      H
   0.321    0.133    0.397 

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: 179
Number of extensions: 5
Number of successful extensions: 3
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: 257
Length of database: 263
Length adjustment: 24
Effective length of query: 233
Effective length of database: 239
Effective search space:    55687
Effective search space used:    55687
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_RS20640 HSERO_RS20640 (enoyl-CoA hydratase)
to HMM TIGR02280 (paaB: phenylacetate degradation probable enoyl-CoA hydratase PaaB (EC 4.2.1.17))

# 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/TIGR02280.hmm
# target sequence database:        /tmp/gapView.4002.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02280  [M=256]
Accession:   TIGR02280
Description: PaaB1: phenylacetate degradation probable enoyl-CoA hydratase PaaB
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.9e-128  412.0   0.4   5.5e-128  411.8   0.4    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS20640  HSERO_RS20640 enoyl-CoA hydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS20640  HSERO_RS20640 enoyl-CoA hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.8   0.4  5.5e-128  5.5e-128       1     256 []       6     263 .]       6     263 .] 0.99

  Alignments for each domain:
  == domain 1  score: 411.8 bits;  conditional E-value: 5.5e-128
                                  TIGR02280   1 illelekgvlrltlnrpdklnsfteemhaelaealerverdd.vrallltGaGrGfcaGqdlsernvt 67 
                                                ille ++g++ +tlnrpdklnsft  mh el++a+  ++ d  vr+llltGaGrGfcaGqdl++r v+
  lcl|FitnessBrowser__HerbieS:HSERO_RS20640   6 ILLENRDGIAVITLNRPDKLNSFTVAMHLELRDAIATLQADPsVRVLLLTGAGRGFCAGQDLGDRAVK 73 
                                                799999***********************************99************************* PP

                                  TIGR02280  68 kg.aapdlGetvekfynplvrrlaalpkpvvvavnGvaaGaGanlalagdivlaaesakfiqafaklG 134
                                                +g +  dlGe+++k+y+plv+ l+alp pv++avnGvaaGaGanl la+divlaa+sa+f+  f+klG
  lcl|FitnessBrowser__HerbieS:HSERO_RS20640  74 PGdDGVDLGESIDKYYGPLVKSLRALPFPVICAVNGVAAGAGANLPLACDIVLAARSASFVEVFCKLG 141
                                                *98999************************************************************** PP

                                  TIGR02280 135 lipdsGGtwllprlvGrarakglallgekldaetaaewGliwqvvddealadevqalaahlakqptrg 202
                                                lipd+GGt++lprlvG+ara+g+allgek++ae+a+ wGliw++vdd++l++e++a+aah+a++pt+g
  lcl|FitnessBrowser__HerbieS:HSERO_RS20640 142 LIPDTGGTYFLPRLVGTARAMGMALLGEKISAEQAERWGLIWKCVDDDQLMEEAHAMAAHFARAPTKG 209
                                                ******************************************************************** PP

                                  TIGR02280 203 lalikralqaaetnsldtqldlerdlqrelGrsadyaeGvaafldkrepefkGk 256
                                                la++k +l a+++++l +qldlerd +r lGrs+dy+eGv+afl+kr p+f+G+
  lcl|FitnessBrowser__HerbieS:HSERO_RS20640 210 LAATKATLYASPAHTLPEQLDLERDTMRALGRSRDYREGVTAFLEKRAPQFTGQ 263
                                                ****************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (263 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 7.06
//
[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