Alignments for a candidate for gloB in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloB in Dechlorosoma suillum PS

Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate Dsui_2484 Dsui_2484 hydroxyacylglutathione hydrolase

Query= CharProtDB::CH_024825
         (251 letters)



>FitnessBrowser__PS:Dsui_2484
          Length = 267

 Score =  189 bits (479), Expect = 6e-53
 Identities = 110/257 (42%), Positives = 144/257 (56%), Gaps = 11/257 (4%)

Query: 3   LNSIPAFDDNYIWVLNDEAGRCLIVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHVGGV 62
           +++IPAF DNYIW+L     R L+VDPGDA PV   +A    + EAI LTHHH DH GGV
Sbjct: 14  ISAIPAFKDNYIWLLQ-RGDRALVVDPGDAAPVQAFLAREGLRLEAILLTHHHADHSGGV 72

Query: 63  KELVEKFPQIVVYGPQETQDKGTTQVVKDGETAFV--LGHEFSVIATPGHTLGHICYFSK 120
             L      + V GP      G  + ++ GE      LG +  V+A PGHT GH+ Y+ +
Sbjct: 73  AALAGD--GVRVLGPAAESITGVGEPLRGGERLEFADLGLQLQVLAVPGHTRGHLAYYGQ 130

Query: 121 ----PYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMKFAL 176
               P LFCGDTLF  GCGRLFEGT +QM  SL  L+ LP  T V CAHEYT +N+ FAL
Sbjct: 131 WEGAPVLFCGDTLFGAGCGRLFEGTPAQMAHSLDLLAVLPPQTAVYCAHEYTAANLDFAL 190

Query: 177 SILPHDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEET--LL 234
           ++ P + ++ +  RKV  +R   Q T+P+ L  E   N FLR  + ++      +    L
Sbjct: 191 AVEPGNRALAERVRKVAAMRQAGQATVPLCLAEELATNPFLRCGEAEVRASAERQAGHAL 250

Query: 235 QQPEERFAWLRSKKDRF 251
                 FA LR  K+ F
Sbjct: 251 TDEVAVFAALREWKNHF 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: 208
Number of extensions: 12
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: 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 Dsui_2484 Dsui_2484 (hydroxyacylglutathione hydrolase)
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.24928.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.3e-100  319.6   0.0   7.1e-100  319.4   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_2484  Dsui_2484 hydroxyacylglutathione


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2484  Dsui_2484 hydroxyacylglutathione hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.4   0.0  7.1e-100  7.1e-100       1     248 []      14     267 .]      14     267 .] 0.97

  Alignments for each domain:
  == domain 1  score: 319.4 bits;  conditional E-value: 7.1e-100
                         TIGR03413   1 iiaipalsdNyiwllkdekseavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfpvkvvgpaee 77 
                                       i aipa++dNyiwll++ + +a+vvDpg+a+pv+++l+++gl+leaillTHhHaDH ggva+l  + +v+v+gpa+e
  lcl|FitnessBrowser__PS:Dsui_2484  14 ISAIPAFKDNYIWLLQRGD-RALVVDPGDAAPVQAFLAREGLRLEAILLTHHHADHSGGVAALAGD-GVRVLGPAAE 88 
                                       678****************.******************************************9764.79******** PP

                         TIGR03413  78 ripgltkevkegdevel..lelevevlevpGHtlgHiayyleee..kvlFcgDtLfsaGCGrlfegtaeqmleslqk 150
                                       +i+g+ ++++ g+++e+  l+l+++vl+vpGHt+gH+ayy + e  +vlFcgDtLf+aGCGrlfegt++qm +sl+ 
  lcl|FitnessBrowser__PS:Dsui_2484  89 SITGVGEPLRGGERLEFadLGLQLQVLAVPGHTRGHLAYYGQWEgaPVLFCGDTLFGAGCGRLFEGTPAQMAHSLDL 165
                                       *****************777899*****************9977779****************************** PP

                         TIGR03413 151 laaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLraeeaevkaal 227
                                       la Lp +t+vycaHEYt++Nl+Falavep n+al+er+++v+a+r++g++t+P  laee+atNpFLr+ eaev+a++
  lcl|FitnessBrowser__PS:Dsui_2484 166 LAVLPPQTAVYCAHEYTAANLDFALAVEPGNRALAERVRKVAAMRQAGQATVPLCLAEELATNPFLRCGEAEVRASA 242
                                       **************************************************************************999 PP

                         TIGR03413 228 ee....ekaeevevfaelRekkdkf 248
                                       e+    + ++ev+vfa+lRe+k++f
  lcl|FitnessBrowser__PS:Dsui_2484 243 ERqaghALTDEVAVFAALREWKNHF 267
                                       988888899**************98 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: 00:00:00.00
# Mc/sec: 8.63
//
[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