Alignments for a candidate for gloB in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloB in Herbaspirillum seropedicae SmR1

Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate HSERO_RS17120 HSERO_RS17120 hydroxyacylglutathione hydrolase

Query= CharProtDB::CH_024825
         (251 letters)



>FitnessBrowser__HerbieS:HSERO_RS17120
          Length = 264

 Score =  209 bits (531), Expect = 6e-59
 Identities = 119/265 (44%), Positives = 162/265 (61%), Gaps = 16/265 (6%)

Query: 1   MNLNSIPAFDDNYIWVLNDEAGR-CLIVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHV 59
           +++ ++PAFDDNY+W+++D  GR   +VDPGDA PVL A+ A      AI LTHHH DHV
Sbjct: 1   LDVLAVPAFDDNYLWIIHD--GRYAAVVDPGDAVPVLAALQAEGLTLAAILLTHHHADHV 58

Query: 60  GGVKELVEK-----FPQIVVYGPQETQD--KGTTQVV--KDGETAFVLGHEFSVIATPGH 110
           GGV EL  +     FP I VYGP   Q   KG T  +   D     VLG    VI  PGH
Sbjct: 59  GGVVELARQAASDTFPIIPVYGPAREQSRIKGMTVPLHGNDQVDIAVLGLRLEVIEVPGH 118

Query: 111 TLGHICYFS--KPYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYT 168
           T+GHI Y +  +  LFCGDTLF+GGCGRLFEGT  QM  SL +L++LP  T V CAHEYT
Sbjct: 119 TMGHIAYHAPEQAMLFCGDTLFAGGCGRLFEGTPQQMVDSLSRLASLPGQTAVYCAHEYT 178

Query: 169 LSNMKFALSILPHDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVI 228
           LSN+KFA  + P +  ++    + +  R + + T+P  +  ERQ N FLR  + ++++ +
Sbjct: 179 LSNLKFAAEVEPGNAELHARITRERARRERGEPTVPTSIALERQTNPFLRATEKEILDSL 238

Query: 229 NEETLLQQPEE--RFAWLRSKKDRF 251
            +   L++ +E   FA LR  K+ +
Sbjct: 239 QKAGRLKELDEVSSFAALREWKNSY 263


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: 218
Number of extensions: 13
Number of successful extensions: 5
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: 264
Length adjustment: 24
Effective length of query: 227
Effective length of database: 240
Effective search space:    54480
Effective search space used:    54480
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 HSERO_RS17120 HSERO_RS17120 (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.10846.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.1e-102  327.8   0.0   2.3e-102  327.6   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS17120  HSERO_RS17120 hydroxyacylglutath


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS17120  HSERO_RS17120 hydroxyacylglutathione hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.6   0.0  2.3e-102  2.3e-102       2     248 .]       4     263 ..       3     263 .. 0.95

  Alignments for each domain:
  == domain 1  score: 327.6 bits;  conditional E-value: 2.3e-102
                                  TIGR03413   2 iaipalsdNyiwllkdekseavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellek... 66 
                                                 a+pa++dNy+w+++d +  a+vvDpg+a pvl+al+++gl+l+aillTHhHaDHvggv el ++   
  lcl|FitnessBrowser__HerbieS:HSERO_RS17120   4 LAVPAFDDNYLWIIHDGR-YAAVVDPGDAVPVLAALQAEGLTLAAILLTHHHADHVGGVVELARQaas 70 
                                                589**************9.9******************************************876222 PP

                                  TIGR03413  67 ..fp.vkvvgpaee..ripgltkevkegdevel..lelevevlevpGHtlgHiayyleeekvlFcgDt 127
                                                  fp ++v+gpa+e  ri+g+t++++ +d+v++  l+l++ev+evpGHt+gHiay+++e+ +lFcgDt
  lcl|FitnessBrowser__HerbieS:HSERO_RS17120  71 dtFPiIPVYGPAREqsRIKGMTVPLHGNDQVDIavLGLRLEVIEVPGHTMGHIAYHAPEQAMLFCGDT 138
                                                225699******99999*************9987799******************************* PP

                                  TIGR03413 128 LfsaGCGrlfegtaeqmleslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealr 195
                                                Lf+ GCGrlfegt++qm++sl++la+Lp +t+vycaHEYtlsNl+Fa++vep n++l++r+++ +a+r
  lcl|FitnessBrowser__HerbieS:HSERO_RS17120 139 LFAGGCGRLFEGTPQQMVDSLSRLASLPGQTAVYCAHEYTLSNLKFAAEVEPGNAELHARITRERARR 206
                                                ******************************************************************** PP

                                  TIGR03413 196 akgkptlPstlaeekatNpFLraeeaevkaalee....ekaeevevfaelRekkdkf 248
                                                ++g+pt+P+++a e++tNpFLra e+e+  +l++    ++ +ev+ fa+lRe+k+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS17120 207 ERGEPTVPTSIALERQTNPFLRATEKEILDSLQKagrlKELDEVSSFAALREWKNSY 263
                                                ****************************99999999999999************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (264 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: 00:00:00.01
# Mc/sec: 6.31
//
[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