Alignments for a candidate for gloB in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloB in Shewanella oneidensis MR-1

Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate 201703 SO2563 metallo-beta-lactamase family protein (NCBI ptt file)

Query= CharProtDB::CH_024825
         (251 letters)



>FitnessBrowser__MR1:201703
          Length = 267

 Score =  191 bits (485), Expect = 1e-53
 Identities = 109/266 (40%), Positives = 148/266 (55%), Gaps = 15/266 (5%)

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

Query: 60  GGVKELVEKFPQ-----IVVYGPQETQDKGTTQVVKDGETAFV----LGHEFSVIATPGH 110
           GG+  LV    Q     + VYGPQ    +G    ++   T  +    L     V++ PGH
Sbjct: 62  GGIAALVAYVEQTTGHTLAVYGPQSEAIQGVNIAIEPQITQILHLPFLNSPVQVLSVPGH 121

Query: 111 TLGHICYFSKPYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLS 170
           T GHI Y     LFCGDTLFSGGCGRLFEGT +QM  SL+ L+ALP +T V CAHEYTL+
Sbjct: 122 TAGHIAYLVDGALFCGDTLFSGGCGRLFEGTPAQMCHSLRLLAALPAETRVYCAHEYTLA 181

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

Query: 231 ETLLQQPEE-----RFAWLRSKKDRF 251
           +   Q          F  LR  KD F
Sbjct: 242 QFCDQDLSNVDELTYFTLLRQWKDIF 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: 225
Number of extensions: 10
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 201703 SO2563 (metallo-beta-lactamase family protein (NCBI ptt file))
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.6375.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    7.7e-96  306.2   0.0    8.7e-96  306.0   0.0    1.0  1  lcl|FitnessBrowser__MR1:201703  SO2563 metallo-beta-lactamase fa


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201703  SO2563 metallo-beta-lactamase family protein (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.0   0.0   8.7e-96   8.7e-96       1     248 []       4     267 .]       4     267 .] 0.92

  Alignments for each domain:
  == domain 1  score: 306.0 bits;  conditional E-value: 8.7e-96
                       TIGR03413   1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfp......vkvv 72 
                                     i+ai+a++dNyiw+l+++++ +++vvDpg+ + vl++l++++l+l+ il+THhH+DH+gg+a+l++ ++      ++v+
  lcl|FitnessBrowser__MR1:201703   4 ITAINAFNDNYIWVLQQDTQqAVYVVDPGDVNVVLDYLNAHQLTLAGILITHHHRDHTGGIAALVAYVEqttghtLAVY 82 
                                     689*************99997999***************************************98654333246689** PP

                       TIGR03413  73 gpaeeripgltkevkeg....devellelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGrlfegtaeqmles 147
                                     gp++e+i+g++ +++ +     ++ +l++ v+vl+vpGHt+gHiay+++  ++lFcgDtLfs GCGrlfegt++qm +s
  lcl|FitnessBrowser__MR1:201703  83 GPQSEAIQGVNIAIEPQitqiLHLPFLNSPVQVLSVPGHTAGHIAYLVD--GALFCGDTLFSGGCGRLFEGTPAQMCHS 159
                                     ********9998887552100345569**********************..**************************** PP

                       TIGR03413 148 lqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLraeeaevkaa 226
                                     l+ laaLp+et+vycaHEYtl+Nl+Fa+a++p+n++lk++ ++++alra+gk+t+Pst++ e+++NpFLr  ++++  +
  lcl|FitnessBrowser__MR1:201703 160 LRLLAALPAETRVYCAHEYTLANLKFAQAADPSNAKLKAYNEQATALRAQGKATIPSTIGLERSINPFLRGLTPTIVDS 238
                                     ****************************************************************************999 PP

                       TIGR03413 227 lee.......ekaeevevfaelRekkdkf 248
                                     +++       ++ +e++ f+ lR++kd f
  lcl|FitnessBrowser__MR1:201703 239 IKQqfcdqdlSNVDELTYFTLLRQWKDIF 267
                                     999999999889999************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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.69
//
[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