Alignments for a candidate for garR in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for garR in Azospirillum brasilense Sp245

Align tartronate semialdehyde reductase 2 (characterized)
to candidate AZOBR_RS07955 AZOBR_RS07955 tartronate semialdehyde reductase

Query= ecocyc::G6278-MONOMER
         (292 letters)



>FitnessBrowser__azobra:AZOBR_RS07955
          Length = 302

 Score =  407 bits (1046), Expect = e-118
 Identities = 202/291 (69%), Positives = 239/291 (82%)

Query: 1   MKLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVADELLSLGAVSVETARQVTEASDIIF 60
           M +GFIGLGIMG PMA +LA AGH L V  I P  ++LL+ GA +  ++R+V + +DI+F
Sbjct: 1   MNVGFIGLGIMGRPMAGHLADAGHTLFVYDINPAPEDLLAKGATACGSSREVAQKADIVF 60

Query: 61  IMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVS 120
            MVPDTP V+  LFG NG  +    GK +VDMSSISPIETK FA+++NELG DYLDAPVS
Sbjct: 61  TMVPDTPHVQAALFGPNGVAEGLSAGKIVVDMSSISPIETKAFAQRINELGCDYLDAPVS 120

Query: 121 GGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNI 180
           GGE+GA+  +L+IMVGG +  FE VKPLFE +GKNITLVGGNGDGQT KVANQI+VAL I
Sbjct: 121 GGEVGAKAASLTIMVGGPDKAFETVKPLFEKMGKNITLVGGNGDGQTTKVANQIVVALTI 180

Query: 181 EAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLN 240
           EAV EALLFASKAGADP +VRQALMGGFASSRILEVHGERM+KRTF+PGF+I LHQKDLN
Sbjct: 181 EAVGEALLFASKAGADPAKVRQALMGGFASSRILEVHGERMVKRTFDPGFRIELHQKDLN 240

Query: 241 LALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKL 291
           LAL  A+AL ++LPNTATCQELFN CAA GG   DHS +V+ALEL+ANH++
Sbjct: 241 LALSGARALGVSLPNTATCQELFNACAAQGGKAWDHSGMVRALELLANHEI 291


Lambda     K      H
   0.318    0.135    0.376 

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: 340
Number of extensions: 5
Number of successful extensions: 1
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: 292
Length of database: 302
Length adjustment: 26
Effective length of query: 266
Effective length of database: 276
Effective search space:    73416
Effective search space used:    73416
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate AZOBR_RS07955 AZOBR_RS07955 (tartronate semialdehyde reductase)
to HMM TIGR01505 (2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60))

# 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/TIGR01505.hmm
# target sequence database:        /tmp/gapView.6107.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01505  [M=291]
Accession:   TIGR01505
Description: tartro_sem_red: 2-hydroxy-3-oxopropionate reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.6e-131  421.6   3.2   8.5e-131  421.4   3.2    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS07955  AZOBR_RS07955 tartronate semiald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS07955  AZOBR_RS07955 tartronate semialdehyde reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.4   3.2  8.5e-131  8.5e-131       2     291 .]       3     291 ..       2     291 .. 0.99

  Alignments for each domain:
  == domain 1  score: 421.4 bits;  conditional E-value: 8.5e-131
                                 TIGR01505   2 vgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqve 70 
                                               vgfiGlGimG+Pm+  l+ aG+ l v +++ +a ++lla Ga++ ++ +ev+++ad+++tmvPd+P+v+
  lcl|FitnessBrowser__azobra:AZOBR_RS07955   3 VGFIGLGIMGRPMAGHLADAGHTLFVYDIN-PAPEDLLAKGATACGSSREVAQKADIVFTMVPDTPHVQ 70 
                                               9*****************************.999*********************************** PP

                                 TIGR01505  71 evalGenGileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtlsimvGGdk 139
                                               + ++G+nG+ e+   Gk++vdmssi+P+e+k +a+ ++e+G d+ldaPvsGGe+ga+ + l+imvGG +
  lcl|FitnessBrowser__azobra:AZOBR_RS07955  71 AALFGPNGVAEGLSAGKIVVDMSSISPIETKAFAQRINELGCDYLDAPVSGGEVGAKAASLTIMVGGPD 139
                                               ********************************************************************* PP

                                 TIGR01505 140 avfdkvkpllealgksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGl 208
                                                 f+ vkpl+e +gk+i+lvG+nG+Gqt+kvanq++val ieav eal++a+kaG+dp +v+qal+GG+
  lcl|FitnessBrowser__azobra:AZOBR_RS07955 140 KAFETVKPLFEKMGKNITLVGGNGDGQTTKVANQIVVALTIEAVGEALLFASKAGADPAKVRQALMGGF 208
                                               ********************************************************************* PP

                                 TIGR01505 209 agstvleakkerlldrdfkPGfridlhqkdlalaldaakavgaalPvtavvaellaalradGdgtldhs 277
                                               a+s++le+++er+++r+f+PGfri+lhqkdl+lal  a+a+g++lP+ta+++el++a++a+G+   dhs
  lcl|FitnessBrowser__azobra:AZOBR_RS07955 209 ASSRILEVHGERMVKRTFDPGFRIELHQKDLNLALSGARALGVSLPNTATCQELFNACAAQGGKAWDHS 277
                                               ********************************************************************* PP

                                 TIGR01505 278 alvraleklakdkv 291
                                                +vrale+la++++
  lcl|FitnessBrowser__azobra:AZOBR_RS07955 278 GMVRALELLANHEI 291
                                               ***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (291 nodes)
Target sequences:                          1  (302 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: 00:00:00.00
# Mc/sec: 11.35
//
[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