Alignments for a candidate for gloB in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloB in Shewanella loihica PV-4

Align hydroxyacylglutathione hydrolase (EC 3.1.2.6) (characterized)
to candidate 5209661 Shew_2114 hydroxyacylglutathione hydrolase (RefSeq)

Query= BRENDA::Q8ZRM2
         (251 letters)



>FitnessBrowser__PV4:5209661
          Length = 260

 Score =  195 bits (495), Expect = 9e-55
 Identities = 109/254 (42%), Positives = 147/254 (57%), Gaps = 9/254 (3%)

Query: 6   IPAFQDNYIWVL-TNDEGRCVIVDPGEAAPVLKAIAEHKWMPEAIFLTHHHHDHVGGVKE 64
           IPAF DNYIW++   D G   +VDPG+A  VL  + +H+ + + I +THHH DH GG+ E
Sbjct: 7   IPAFNDNYIWLIHAKDSGGHYVVDPGDAKAVLDYLEQHQIVLDGILITHHHSDHTGGIAE 66

Query: 65  L-LQHFPQMTVYGPAETQDKGATHLVGDGDTIRVLGEKF----TLFATPGHTLGHVCYFS 119
           L   H  ++TVYGP     KG  H +  G T  V  EK      +F  PGHTLGH+ Y  
Sbjct: 67  LQASHDHKLTVYGPDNENIKGINHPIS-GQTESVKPEKLDSDAAVFHLPGHTLGHIAYLI 125

Query: 120 RPYLFCGDTLFSGGCGRLFEGTPSQMYQSLMKINSLPDDTLICCAHEYTLANIKFALSIL 179
             +LFCGDTLFS GCGRLFEGTP+QM+ SL  +  L + TL+  AHEYT AN+ FAL++ 
Sbjct: 126 DDHLFCGDTLFSAGCGRLFEGTPAQMHHSLQTLAQLDETTLVYPAHEYTQANLAFALTVE 185

Query: 180 PHDSFINEYYRKVKELRVKKQMTLPVILKNERKINLFLRTEDIDLINEINKETI--LQQP 237
             +  +  +  KVK+LR +   +LP  +  E++IN FLR E   +   ++      +   
Sbjct: 186 NDNEALIAHAAKVKQLRDQNLPSLPSSIGLEKQINPFLRPEQASIKQNLSCHFAQDVTDD 245

Query: 238 EARFAWLRSKKDTF 251
              F  LR  KD F
Sbjct: 246 GTSFTLLRQWKDNF 259


Lambda     K      H
   0.323    0.140    0.436 

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: 252
Number of extensions: 15
Number of successful extensions: 4
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: 260
Length adjustment: 24
Effective length of query: 227
Effective length of database: 236
Effective search space:    53572
Effective search space used:    53572
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate 5209661 Shew_2114 (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.14082.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    8.8e-99  315.9   0.4      1e-98  315.7   0.4    1.0  1  lcl|FitnessBrowser__PV4:5209661  Shew_2114 hydroxyacylglutathione


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209661  Shew_2114 hydroxyacylglutathione hydrolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.7   0.4     1e-98     1e-98       1     248 []       4     259 ..       4     259 .. 0.95

  Alignments for each domain:
  == domain 1  score: 315.7 bits;  conditional E-value: 1e-98
                        TIGR03413   1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfp..vkvvgpa 75 
                                      +++ipa++dNyiwl++ ++s   +vvDpg+a+ vl++le++++ l+ il+THhH+DH+gg+ael+++++  ++v+gp+
  lcl|FitnessBrowser__PV4:5209661   4 VTPIPAFNDNYIWLIHAKDSgGHYVVDPGDAKAVLDYLEQHQIVLDGILITHHHSDHTGGIAELQASHDhkLTVYGPD 81 
                                      579*****************9********************************************998878******* PP

                        TIGR03413  76 eeripgltkevkeg.devel..lelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGrlfegtaeqmleslqk 150
                                      +e+i+g++++++ + ++v+   l++++ v++ pGHtlgHiay+++  ++lFcgDtLfsaGCGrlfegt++qm++slq 
  lcl|FitnessBrowser__PV4:5209661  82 NENIKGINHPISGQtESVKPekLDSDAAVFHLPGHTLGHIAYLID--DHLFCGDTLFSAGCGRLFEGTPAQMHHSLQT 157
                                      ***********865156665668999*******************..9****************************** PP

                        TIGR03413 151 laaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLraeeaevkaale 228
                                      la+L+e+t+vy+aHEYt++Nl+Fal+ve +neal +++++v++lr+++ p+lPs+++ ek++NpFLr e+a++k++l+
  lcl|FitnessBrowser__PV4:5209661 158 LAQLDETTLVYPAHEYTQANLAFALTVENDNEALIAHAAKVKQLRDQNLPSLPSSIGLEKQINPFLRPEQASIKQNLS 235
                                      ***************************************************************************999 PP

                        TIGR03413 229 e....ekaeevevfaelRekkdkf 248
                                           + +++ + f+ lR++kd+f
  lcl|FitnessBrowser__PV4:5209661 236 ChfaqDVTDDGTSFTLLRQWKDNF 259
                                      8777677888999*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (260 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: 00:00:00.00
# Mc/sec: 9.45
//
[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