Alignments for a candidate for gloB in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloB in Pseudomonas fluorescens FW300-N1B4

Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate Pf1N1B4_4596 Hydroxyacylglutathione hydrolase (EC 3.1.2.6)

Query= CharProtDB::CH_024825
         (251 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4596
          Length = 255

 Score =  227 bits (578), Expect = 2e-64
 Identities = 119/255 (46%), Positives = 160/255 (62%), Gaps = 5/255 (1%)

Query: 1   MNLNSIPAFDDNYIWVLNDEAG-RCLIVDPGDAEPVLNAIAAN-NWQPEAIFLTHHHHDH 58
           + ++++PAF DNYIW+L D +  RC +VDPGDA PV   +AA+  W    I +THHHHDH
Sbjct: 2   IQISALPAFTDNYIWLLQDHSTQRCAVVDPGDAAPVQAWLAAHPGWVLSDILITHHHHDH 61

Query: 59  VGGVKELVEKFPQIVVYGPQETQDKGTTQVVKDGETAFVLGHEFSVIATPGHTLGHICYF 118
           VGGV+ L +K     VYGP           +K+ +   VLG +F VI  PGHTLGHI ++
Sbjct: 62  VGGVERL-KKATDATVYGPASESIPARDVALKNNDRISVLGWDFDVIQVPGHTLGHIAFY 120

Query: 119 SKPYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMKFALSI 178
            + +LFCGDTLF+ GCGRLFEGT  QM+ SL +L+ALP+DTLV C HEYTLSN+KFA ++
Sbjct: 121 HQGHLFCGDTLFAAGCGRLFEGTPEQMHHSLSRLAALPEDTLVYCTHEYTLSNLKFAAAV 180

Query: 179 LPHDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEE--TLLQQ 236
            P +        KV   R    +TLP  L  E++ N FLR ++  +   ++E   T  + 
Sbjct: 181 EPGNPDTAARLEKVTAQREAGLMTLPSTLALEKRTNPFLRVDETSVKEKVDERNGTQNRA 240

Query: 237 PEERFAWLRSKKDRF 251
           P   FA LR+ KD+F
Sbjct: 241 PSAVFAALRAWKDKF 255


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: 251
Number of extensions: 12
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: 255
Length adjustment: 24
Effective length of query: 227
Effective length of database: 231
Effective search space:    52437
Effective search space used:    52437
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: 46 (22.3 bits)

Align candidate Pf1N1B4_4596 (Hydroxyacylglutathione hydrolase (EC 3.1.2.6))
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.17748.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
     4e-109  349.7   0.0   4.6e-109  349.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4596  Hydroxyacylglutathione hydrolase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4596  Hydroxyacylglutathione hydrolase (EC 3.1.2.6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.5   0.0  4.6e-109  4.6e-109       1     248 []       4     255 .]       4     255 .] 0.98

  Alignments for each domain:
  == domain 1  score: 349.5 bits;  conditional E-value: 4.6e-109
                                      TIGR03413   1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeek.glkleaillTHhHaDHvggvae 62 
                                                    i a+pa++dNyiwll+d+++ +++vvDpg+a+pv+++l+++ g+ l++il+THhH+DHvggv++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4596   4 ISALPAFTDNYIWLLQDHSTqRCAVVDPGDAAPVQAWLAAHpGWVLSDILITHHHHDHVGGVER 67 
                                                    5789**************999*****************98879********************* PP

                                      TIGR03413  63 llekfpvkvvgpaeeripgltkevkegdevellelevevlevpGHtlgHiayyleeekvlFcgD 126
                                                    l+++++++v+gpa+e+ip+ ++++k++d++++l+ +++v++vpGHtlgHia+y +  ++lFcgD
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4596  68 LKKATDATVYGPASESIPARDVALKNNDRISVLGWDFDVIQVPGHTLGHIAFYHQ--GHLFCGD 129
                                                    *******************************************************..******* PP

                                      TIGR03413 127 tLfsaGCGrlfegtaeqmleslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlke 190
                                                    tLf+aGCGrlfegt+eqm++sl++laaLpe+t+vyc+HEYtlsNl+Fa+avep n++ ++rl++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4596 130 TLFAAGCGRLFEGTPEQMHHSLSRLAALPEDTLVYCTHEYTLSNLKFAAAVEPGNPDTAARLEK 193
                                                    **************************************************************** PP

                                      TIGR03413 191 vealrakgkptlPstlaeekatNpFLraeeaevkaalee....ekaeevevfaelRekkdkf 248
                                                    v+a+r++g +tlPstla ek+tNpFLr++e++vk++++e    +++ + +vfa+lR++kdkf
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4596 194 VTAQREAGLMTLPSTLALEKRTNPFLRVDETSVKEKVDErngtQNRAPSAVFAALRAWKDKF 255
                                                    *************************************99999899999************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (255 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 7.45
//
[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