Alignments for a candidate for gloB in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloB in Shewanella amazonensis SB2B

Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate 6937743 Sama_1884 hydroxyacylglutathione hydrolase (RefSeq)

Query= CharProtDB::CH_024825
         (251 letters)



>FitnessBrowser__SB2B:6937743
          Length = 258

 Score =  213 bits (541), Expect = 4e-60
 Identities = 116/259 (44%), Positives = 157/259 (60%), Gaps = 10/259 (3%)

Query: 1   MNLNSIPAFDDNYIWVLNDEAGRCLIVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHVG 60
           +++  IPAF DNYIW++    G  ++VDPGDA PV+N +   N Q  A+ LTHHH DH G
Sbjct: 2   LDIRPIPAFADNYIWMIVLPDGGAVVVDPGDAMPVINTLQRLNLQLTAVLLTHHHRDHNG 61

Query: 61  GVKELVE----KFPQIVVYGPQETQDKGTTQVVKDGETAFVLG--HEFSVIATPGHTLGH 114
           G+ +L +          VYG   T D     + +DG+T  + G      V++ PGHTL H
Sbjct: 62  GINQLRDWAKSNGQSFTVYGAV-TSDYSDV-LCRDGDTVDISGLTSPVRVLSVPGHTLDH 119

Query: 115 ICYFSKPYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMKF 174
           + +     LFCGDTLFSGGCGRLFEG A Q+Y SL KL++LPDDTLV CAHEYTLSN++F
Sbjct: 120 LAFVVDNALFCGDTLFSGGCGRLFEGDAGQLYDSLAKLASLPDDTLVYCAHEYTLSNLRF 179

Query: 175 ALSILPHDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEETLL 234
           AL++ P +  + DY ++V  LR  N+ +LP  L  E+ IN FLR +   +   +  +   
Sbjct: 180 ALAVEPQNQCLQDYVKQVNNLREANKPSLPSTLGTEKAINPFLRVDTATVHAAVAAQAGQ 239

Query: 235 QQPEE--RFAWLRSKKDRF 251
           + P+E    A LR  KD F
Sbjct: 240 KVPDEVTCLALLRRWKDNF 258


Lambda     K      H
   0.321    0.138    0.425 

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: 243
Number of extensions: 15
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: 251
Length of database: 258
Length adjustment: 24
Effective length of query: 227
Effective length of database: 234
Effective search space:    53118
Effective search space used:    53118
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: 47 (22.7 bits)

Align candidate 6937743 Sama_1884 (hydroxyacylglutathione hydrolase (RefSeq))
to HMM TIGR03413 (gloB: hydroxyacylglutathione hydrolase (EC 3.1.2.6))

# 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/TIGR03413.hmm
# target sequence database:        /tmp/gapView.30374.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03413  [M=248]
Accession:   TIGR03413
Description: GSH_gloB: hydroxyacylglutathione hydrolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    2.3e-96  308.0   0.0    2.5e-96  307.8   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6937743  Sama_1884 hydroxyacylglutathione


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937743  Sama_1884 hydroxyacylglutathione hydrolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.8   0.0   2.5e-96   2.5e-96       1     248 []       4     258 .]       4     258 .] 0.94

  Alignments for each domain:
  == domain 1  score: 307.8 bits;  conditional E-value: 2.5e-96
                         TIGR03413   1 iiaipalsdNyiwllkdekseavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfp.....vkvv 72 
                                       i +ipa++dNyiw++  ++  avvvDpg+a pv+++l++ +l+l+a+llTHhH+DH gg+++l++ ++      +v+
  lcl|FitnessBrowser__SB2B:6937743   4 IRPIPAFADNYIWMIVLPDGGAVVVDPGDAMPVINTLQRLNLQLTAVLLTHHHRDHNGGINQLRDWAKsngqsFTVY 80 
                                       679************************************************************87544334568999 PP

                         TIGR03413  73 gpaeeripgltkevkegdevel..lelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGrlfegtaeqmles 147
                                       g+ +++    ++  ++gd+v++  l++ v+vl+vpGHtl+H+a++++  ++lFcgDtLfs GCGrlfeg+a q+++s
  lcl|FitnessBrowser__SB2B:6937743  81 GAVTSDY--SDVLCRDGDTVDIsgLTSPVRVLSVPGHTLDHLAFVVD--NALFCGDTLFSGGCGRLFEGDAGQLYDS 153
                                       9987655..57999*******97778889******************..9*************************** PP

                         TIGR03413 148 lqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLraeeaevk 224
                                       l kla+Lp++t+vycaHEYtlsNlrFalavep+n+ l++++k+v++lr+++kp+lPstl++eka+NpFLr+++a+v+
  lcl|FitnessBrowser__SB2B:6937743 154 LAKLASLPDDTLVYCAHEYTLSNLRFALAVEPQNQCLQDYVKQVNNLREANKPSLPSTLGTEKAINPFLRVDTATVH 230
                                       ****************************************************************************9 PP

                         TIGR03413 225 aalee....ekaeevevfaelRekkdkf 248
                                       aa+++    +  +ev+++a lR++kd+f
  lcl|FitnessBrowser__SB2B:6937743 231 AAVAAqagqKVPDEVTCLALLRRWKDNF 258
                                       99988788788899************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (258 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.15
//
[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