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.17330.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.03
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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