GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gloB in Azospirillum brasilense Sp245

Align Hydroxyacylglutathione hydrolase cytoplasmic; Glyoxalase II; Glx II; EC 3.1.2.6 (characterized)
to candidate AZOBR_RS20450 AZOBR_RS20450 hydroxyacylglutathione hydrolase

Query= SwissProt::O24496
         (258 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS20450 AZOBR_RS20450
           hydroxyacylglutathione hydrolase
          Length = 253

 Score =  192 bits (487), Expect = 7e-54
 Identities = 104/259 (40%), Positives = 145/259 (55%), Gaps = 9/259 (3%)

Query: 1   MKIFHVPCLQDNYSYLIIDESTGDAAVVDPVDPEKVIASAEKHQAKIKFVLTTHHHWDHA 60
           M I  +P   DNY YL+ D ++G   VVDP D + V+A  E+    +  +  THHH DH 
Sbjct: 1   MDIHLIPAFADNYIYLLRDPASGAVGVVDPGDAQPVLAELERRNWTLTHIFNTHHHNDHI 60

Query: 61  GGNEKIK-QLVPDIKVYGGSLDKVKGCTDAVDNGDKLTLGQDINILALHTPCHTKGHISY 119
           GGN  +K +   D+      + ++      +  G+ ++ G  +       P HT GHI++
Sbjct: 61  GGNHALKARYGADVIGPRADVARIPDMETCLGEGETISFGS-LAAQVFFVPGHTSGHIAF 119

Query: 120 YVNGKEGENPAVFTGDTLFVAGCGKFFEGTAEQMYQSLCVTLAALPKPTQVYCGHEYTVK 179
           +      E  A+F GDTLF  GCG+ FEGT  QM+ SL V L  LP  T+VYCGHEYT+ 
Sbjct: 120 WFT----EAKALFCGDTLFALGCGRLFEGTPAQMWASL-VKLRGLPDDTRVYCGHEYTLS 174

Query: 180 NLEFALTVEPNNGKIQQKLAWARQQRQADLPTIPSTLEEELETNPFMRVDKPEIQEKLGC 239
           N  FA+TVEP+N  ++ + A    QR+   PTIPSTL  E  TNPF+R D PE+Q  LG 
Sbjct: 175 NARFAVTVEPDNAALKARAADIAAQRERGEPTIPSTLGVEKATNPFLRADVPEVQSALGM 234

Query: 240 --KSPIDTMREVRNKKDQW 256
               P+    E+R +KD++
Sbjct: 235 AGADPVAVFAEIRGRKDRF 253


Lambda     K      H
   0.317    0.135    0.411 

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: 193
Number of extensions: 11
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: 258
Length of database: 253
Length adjustment: 24
Effective length of query: 234
Effective length of database: 229
Effective search space:    53586
Effective search space used:    53586
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate AZOBR_RS20450 AZOBR_RS20450 (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.32077.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.9e-109  349.5   0.0   5.5e-109  349.3   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS20450  AZOBR_RS20450 hydroxyacylglutath


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS20450  AZOBR_RS20450 hydroxyacylglutathione hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.3   0.0  5.5e-109  5.5e-109       1     248 []       3     253 .]       3     253 .] 0.99

  Alignments for each domain:
  == domain 1  score: 349.3 bits;  conditional E-value: 5.5e-109
                                 TIGR03413   1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfp 68 
                                               i+ ipa++dNyi+ll+d++s ++ vvDpg+a+pvl+ le+++++l++i++THhH+DH+gg+++l+++++
  lcl|FitnessBrowser__azobra:AZOBR_RS20450   3 IHLIPAFADNYIYLLRDPASgAVGVVDPGDAQPVLAELERRNWTLTHIFNTHHHNDHIGGNHALKARYG 71 
                                               688*****************9999********************************************* PP

                                 TIGR03413  69 vkvvgpaee..ripgltkevkegdevellelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGr 135
                                               ++v+gp+++  rip +++ + eg+++++++l+++v+ vpGHt+gHia++++e+k+lFcgDtLf++GCGr
  lcl|FitnessBrowser__azobra:AZOBR_RS20450  72 ADVIGPRADvaRIPDMETCLGEGETISFGSLAAQVFFVPGHTSGHIAFWFTEAKALFCGDTLFALGCGR 140
                                               *********99********************************************************** PP

                                 TIGR03413 136 lfegtaeqmleslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPs 204
                                               lfegt++qm++sl kl+ Lp++t+vyc+HEYtlsN+rFa++vep+n+alk+r+++++a+r++g+pt+Ps
  lcl|FitnessBrowser__azobra:AZOBR_RS20450 141 LFEGTPAQMWASLVKLRGLPDDTRVYCGHEYTLSNARFAVTVEPDNAALKARAADIAAQRERGEPTIPS 209
                                               ********************************************************************* PP

                                 TIGR03413 205 tlaeekatNpFLraeeaevkaaleeekaeevevfaelRekkdkf 248
                                               tl+ ekatNpFLra+ +ev++al+++ a++v+vfae+R +kd+f
  lcl|FitnessBrowser__azobra:AZOBR_RS20450 210 TLGVEKATNPFLRADVPEVQSALGMAGADPVAVFAEIRGRKDRF 253
                                               ******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (253 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: 10.28
//
[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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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