Alignments for a candidate for gloB in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloB in Phaeobacter inhibens BS107

Align Hydroxyacylglutathione hydrolase; EC 3.1.2.6; Glyoxalase II; Glx II (uncharacterized)
to candidate GFF2482 PGA1_c25140 hydroxyacylglutathione hydrolase GloB

Query= curated2:Q162S3
         (255 letters)



>FitnessBrowser__Phaeo:GFF2482
          Length = 257

 Score =  309 bits (792), Expect = 3e-89
 Identities = 153/255 (60%), Positives = 189/255 (74%)

Query: 1   MPIEILTIPCLNDNYAFLVHDTATGQTALIDVPEAAPILKVLAERTWQLSEVWITHHHAD 60
           MP+EI+T+PCL+DNYAFL+H+  TG+TAL+D PEAA I   L  R W L ++ +THHH D
Sbjct: 3   MPLEIVTLPCLSDNYAFLLHNAETGRTALVDAPEAAAIRSELERRGWGLDQILLTHHHWD 62

Query: 61  HVQGLGDILSAHPAQVRGAARDAHRLPALDVELRDGESFDFAGHKVDVMDVSGHTVGHIA 120
           H+ G+ D+ +A+  QV GA+ DAHRLP LD+ + +G+SF     +V V+DVSGHT+GHIA
Sbjct: 63  HIDGVADLRTAYDPQVIGASADAHRLPDLDLAVAEGDSFTCLDEEVSVLDVSGHTIGHIA 122

Query: 121 YYCADAKAVFTADSLMALGCGRLFEGTADQMWDSLSKLAALPSETQVYSGHEYTAANARF 180
           ++   A AVFTADSLMALGCGRLFEGT DQMW SL KL+ALP ET VYSGHEYT +NARF
Sbjct: 123 FHIPSAAAVFTADSLMALGCGRLFEGTPDQMWQSLQKLSALPGETTVYSGHEYTQSNARF 182

Query: 181 ALTIDPHNPDLISRSEGITAARAAAKPTVPSTLATEAATNPFLRAADPAIRAHLNMQHAS 240
           ALTI+P N  L  R + I AARA  + TVPS L  E  TNPFLRA   +++  + M  AS
Sbjct: 183 ALTIEPDNAALQHRCKAIDAARAKGEATVPSQLQEELDTNPFLRAHLDSLKQAVGMTGAS 242

Query: 241 DSEVFAEIRARKDAF 255
            +EVFAEIRARKD F
Sbjct: 243 AAEVFAEIRARKDKF 257


Lambda     K      H
   0.319    0.131    0.394 

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: 8
Number of successful extensions: 1
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: 255
Length of database: 257
Length adjustment: 24
Effective length of query: 231
Effective length of database: 233
Effective search space:    53823
Effective search space used:    53823
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 GFF2482 PGA1_c25140 (hydroxyacylglutathione hydrolase GloB)
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.24951.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-102  325.9   0.0   8.7e-102  325.7   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2482  PGA1_c25140 hydroxyacylglutathio


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2482  PGA1_c25140 hydroxyacylglutathione hydrolase GloB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.7   0.0  8.7e-102  8.7e-102       1     248 []       7     257 .]       7     257 .] 0.99

  Alignments for each domain:
  == domain 1  score: 325.7 bits;  conditional E-value: 8.7e-102
                          TIGR03413   1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfpvkvvgpa 75 
                                        i+++p+lsdNy++ll+++++ ++++vD++ea+ + + le++g+ l++illTHhH+DH++gva+l+++++ +v+g++
  lcl|FitnessBrowser__Phaeo:GFF2482   7 IVTLPCLSDNYAFLLHNAETgRTALVDAPEAAAIRSELERRGWGLDQILLTHHHWDHIDGVADLRTAYDPQVIGAS 82 
                                        6789****************9******************************************************9 PP

                          TIGR03413  76 ee..ripgltkevkegdevellelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGrlfegtaeqmleslq 149
                                        ++  r+p l+ +v+egd++++l++ev+vl+v+GHt gHia++++++ ++F++D+L+++GCGrlfegt++qm++slq
  lcl|FitnessBrowser__Phaeo:GFF2482  83 ADahRLPDLDLAVAEGDSFTCLDEEVSVLDVSGHTIGHIAFHIPSAAAVFTADSLMALGCGRLFEGTPDQMWQSLQ 158
                                        99899*********************************************************************** PP

                          TIGR03413 150 klaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLraeeaevka 225
                                        kl+aLp et+vy++HEYt+sN+rFal++ep+n+al++r k+++a+rakg++t+Ps+l+ee++tNpFLra+  ++k+
  lcl|FitnessBrowser__Phaeo:GFF2482 159 KLSALPGETTVYSGHEYTQSNARFALTIEPDNAALQHRCKAIDAARAKGEATVPSQLQEELDTNPFLRAHLDSLKQ 234
                                        **************************************************************************** PP

                          TIGR03413 226 aleeekaeevevfaelRekkdkf 248
                                        a++++ a+++evfae+R++kdkf
  lcl|FitnessBrowser__Phaeo:GFF2482 235 AVGMTGASAAEVFAEIRARKDKF 257
                                        *********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (257 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.93
//
[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