Alignments for a candidate for garR in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for garR in Desulfovibrio vulgaris Miyazaki F

Align 2-hydroxy-3-oxopropionate reductase; Tartronate semialdehyde reductase; TSAR; EC 1.1.1.60 (characterized)
to candidate 8502217 DvMF_2927 tartronate semialdehyde reductase (RefSeq)

Query= SwissProt::P0ABQ2
         (294 letters)



>FitnessBrowser__Miya:8502217
          Length = 299

 Score =  365 bits (936), Expect = e-106
 Identities = 192/293 (65%), Positives = 222/293 (75%)

Query: 2   KVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVII 61
           ++GFIGLGIMG PM +NLLKAG+ +    RN + +  + A GA  A +  A+A   DV+I
Sbjct: 3   RIGFIGLGIMGAPMCRNLLKAGFPVTAYTRNGDKLRAMAAEGAAAAESPAAVAAASDVVI 62

Query: 62  TMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLDAPVS 121
           TMLPNSP V+ VALG  GI EGA PG ++ DMSSIAPLASREI+  L  K I MLDAPVS
Sbjct: 63  TMLPNSPEVRAVALGPGGIAEGAAPGCIVADMSSIAPLASREIAAELAKKSIRMLDAPVS 122

Query: 122 GGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGEIGAGNVTKLANQVIVALNI 181
           GGEPKAIDGTLSVMVGG +  FD    + KAMA SVV  GE+GAGNVTKLANQ++VA NI
Sbjct: 123 GGEPKAIDGTLSVMVGGAQEDFDACLPVFKAMAASVVRVGEVGAGNVTKLANQIVVAGNI 182

Query: 182 AAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDLA 241
           AAMSEAL LAT+AG +PDLVYQAIRGGLAGSTVLDAKAP+VMD  F PGFRI LH KD+ 
Sbjct: 183 AAMSEALVLATRAGADPDLVYQAIRGGLAGSTVLDAKAPLVMDGRFTPGFRIRLHAKDMG 242

Query: 242 NALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALACYYEKLAKVEVTR 294
           N L+TS  +   LPL A +ME+MQ L ADGLG ADH AL  ++EKLA VEV R
Sbjct: 243 NVLETSRELHVPLPLAAQLMEVMQGLMADGLGDADHGALIRHWEKLAGVEVRR 295


Lambda     K      H
   0.316    0.133    0.366 

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: 329
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: 294
Length of database: 299
Length adjustment: 26
Effective length of query: 268
Effective length of database: 273
Effective search space:    73164
Effective search space used:    73164
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: 48 (23.1 bits)

Align candidate 8502217 DvMF_2927 (tartronate semialdehyde reductase (RefSeq))
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.21809.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.4e-122  393.2   9.1   3.8e-122  393.0   9.1    1.0  1  lcl|FitnessBrowser__Miya:8502217  DvMF_2927 tartronate semialdehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8502217  DvMF_2927 tartronate semialdehyde reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.0   9.1  3.8e-122  3.8e-122       1     291 []       3     293 ..       3     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: 393.0 bits;  conditional E-value: 3.8e-122
                         TIGR01505   1 kvgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqveevalGen 77 
                                       ++gfiGlGimG Pm++nllkaG+ +++ t++ ++l  ++a Ga +ae+ ++v+ ++dv++tm+P+sP+v++valG+ 
  lcl|FitnessBrowser__Miya:8502217   3 RIGFIGLGIMGAPMCRNLLKAGFPVTAYTRNGDKLRAMAAEGAAAAESPAAVAAASDVVITMLPNSPEVRAVALGPG 79 
                                       58*************************************************************************** PP

                         TIGR01505  78 GileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtlsimvGGdkavfdkvkpllealgk 154
                                       Gi e+a +G ++ dmssiaPl+s+e+a ++ +k i++ldaPvsGGe++ai+gtls+mvGG + +fd   p+++a++ 
  lcl|FitnessBrowser__Miya:8502217  80 GIAEGAAPGCIVADMSSIAPLASREIAAELAKKSIRMLDAPVSGGEPKAIDGTLSVMVGGAQEDFDACLPVFKAMAA 156
                                       ***************************************************************************** PP

                         TIGR01505 155 sivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGlagstvleakkerlldrdfkPGfr 231
                                       s+v vGe GaG+++k+anq++va ni+a+sealvla++aG+dp++v+qa+rGGlagstvl+ak++ ++d  f PGfr
  lcl|FitnessBrowser__Miya:8502217 157 SVVRVGEVGAGNVTKLANQIVVAGNIAAMSEALVLATRAGADPDLVYQAIRGGLAGSTVLDAKAPLVMDGRFTPGFR 233
                                       ***************************************************************************** PP

                         TIGR01505 232 idlhqkdlalaldaakavgaalPvtavvaellaalradGdgtldhsalvraleklakdkv 291
                                       i lh kd++++l++++++ + lP++a  +e+++ l adG g++dh al+r  ekla+++v
  lcl|FitnessBrowser__Miya:8502217 234 IRLHAKDMGNVLETSRELHVPLPLAAQLMEVMQGLMADGLGDADHGALIRHWEKLAGVEV 293
                                       ********************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (291 nodes)
Target sequences:                          1  (299 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: 8.90
//
[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