Alignments for a candidate for gloB in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloB in Shewanella sp. ANA-3

Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate 7025208 Shewana3_2369 beta-lactamase domain-containing protein (RefSeq)

Query= CharProtDB::CH_024825
         (251 letters)



>FitnessBrowser__ANA3:7025208
          Length = 267

 Score =  203 bits (517), Expect = 3e-57
 Identities = 113/266 (42%), Positives = 153/266 (57%), Gaps = 15/266 (5%)

Query: 1   MNLNSIPAFDDNYIWVLNDEAGRCL-IVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHV 59
           + + +I AF+DNYIWVL  ++ + + +VDPGDA  VL+ + A       I +THHH DH 
Sbjct: 2   LTITAINAFNDNYIWVLRQDSQQAVYVVDPGDANVVLDYLHAQRLSLAGILITHHHRDHT 61

Query: 60  GGVKELVEKFPQ-----IVVYGPQETQDKGTTQVVK----DGETAFVLGHEFSVIATPGH 110
           GG+  L +   Q     + VYGPQ    +G  Q ++    D  T   +     +++ PGH
Sbjct: 62  GGIAALTDHVKQTTGHDLAVYGPQSEDIQGINQPIEPTLSDSLTLPFIDAPVRILSVPGH 121

Query: 111 TLGHICYFSKPYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLS 170
           T GHI Y     LFCGDTLFS GCGRLFEGT SQM+QSL  L+ALPD+T V CAHEYTLS
Sbjct: 122 TAGHIAYLVDDALFCGDTLFSAGCGRLFEGTPSQMWQSLSLLAALPDETRVYCAHEYTLS 181

Query: 171 NMKFALSILPHDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINE 230
           N+KFA ++   + ++N Y  +   LRA+ + T+P  +  ER IN FLR     ++N I  
Sbjct: 182 NLKFAQTVDTDNEALNAYVEEASTLRAQGKATIPSTIGLERAINPFLRPLSPTIVNSIKN 241

Query: 231 ETLLQQPEER-----FAWLRSKKDRF 251
           +   Q   +      F  LR  KD F
Sbjct: 242 QFCDQDLTKADELTCFTLLRQWKDIF 267


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: 233
Number of extensions: 9
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: 251
Length of database: 267
Length adjustment: 24
Effective length of query: 227
Effective length of database: 243
Effective search space:    55161
Effective search space used:    55161
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 7025208 Shewana3_2369 (beta-lactamase domain-containing protein (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.32686.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    3.5e-99  317.2   0.0      4e-99  317.0   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7025208  Shewana3_2369 beta-lactamase dom


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7025208  Shewana3_2369 beta-lactamase domain-containing protein (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.0   0.0     4e-99     4e-99       1     248 []       4     267 .]       4     267 .] 0.93

  Alignments for each domain:
  == domain 1  score: 317.0 bits;  conditional E-value: 4e-99
                         TIGR03413   1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfp......vk 70 
                                       i+ai+a++dNyiw+l+++++ +++vvDpg+a+ vl++l++++l+l+ il+THhH+DH+gg+a+l+++++      ++
  lcl|FitnessBrowser__ANA3:7025208   4 ITAINAFNDNYIWVLRQDSQqAVYVVDPGDANVVLDYLHAQRLSLAGILITHHHRDHTGGIAALTDHVKqttghdLA 80 
                                       689*************99997999***************************************98876543345689 PP

                         TIGR03413  71 vvgpaeeripgltkevke..gdevel..lelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGrlfegtaeq 143
                                       v+gp++e+i+g++++++    d+++l   ++ v++l+vpGHt+gHiay+++  ++lFcgDtLfsaGCGrlfegt++q
  lcl|FitnessBrowser__ANA3:7025208  81 VYGPQSEDIQGINQPIEPtlSDSLTLpfIDAPVRILSVPGHTAGHIAYLVD--DALFCGDTLFSAGCGRLFEGTPSQ 155
                                       ***********999886422455555549**********************..9*********************** PP

                         TIGR03413 144 mleslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLraee 220
                                       m++sl+ laaLp+et+vycaHEYtlsNl+Fa++v+ +neal+++++e+++lra+gk+t+Pst++ e+a+NpFLr  +
  lcl|FitnessBrowser__ANA3:7025208 156 MWQSLSLLAALPDETRVYCAHEYTLSNLKFAQTVDTDNEALNAYVEEASTLRAQGKATIPSTIGLERAINPFLRPLS 232
                                       ***************************************************************************** PP

                         TIGR03413 221 aevkaalee.......ekaeevevfaelRekkdkf 248
                                       +++ +++++       +ka+e+++f+ lR++kd f
  lcl|FitnessBrowser__ANA3:7025208 233 PTIVNSIKNqfcdqdlTKADELTCFTLLRQWKDIF 267
                                       *****99999999999999**************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (267 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: 6.14
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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