Alignments for a candidate for garR in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for garR in Klebsiella michiganensis M5al

Align tartronate semialdehyde reductase 2 (characterized)
to candidate BWI76_RS07000 BWI76_RS07000 2-hydroxy-3-oxopropionate reductase

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



>FitnessBrowser__Koxy:BWI76_RS07000
          Length = 292

 Score =  504 bits (1298), Expect = e-148
 Identities = 254/292 (86%), Positives = 273/292 (93%)

Query: 1   MKLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVADELLSLGAVSVETARQVTEASDIIF 60
           MKLGFIGLGIMGTPMA+ LA+AGH LHVTTIGPVA+ELL  GA  + TA QV E S+IIF
Sbjct: 1   MKLGFIGLGIMGTPMALRLAKAGHALHVTTIGPVAEELLKQGAQHLATAEQVAEQSEIIF 60

Query: 61  IMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVS 120
           IMVPDTPQV +VLFGE+GC KA+LKGKTIVDMSSISPIETKRFA+QV +LG DYLDAPVS
Sbjct: 61  IMVPDTPQVADVLFGEHGCAKAALKGKTIVDMSSISPIETKRFAQQVRDLGADYLDAPVS 120

Query: 121 GGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNI 180
           GGEIGAREGTLSIMVGGDE VF RVKPLF++LGKNITLVGGNGDGQTCKVANQIIVALNI
Sbjct: 121 GGEIGAREGTLSIMVGGDENVFARVKPLFDILGKNITLVGGNGDGQTCKVANQIIVALNI 180

Query: 181 EAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLN 240
           EAVSEAL+FASKAGADP RVRQALMGGFASSRILEVHGERM+ RTFNPGFKI+LHQKDLN
Sbjct: 181 EAVSEALVFASKAGADPARVRQALMGGFASSRILEVHGERMLNRTFNPGFKISLHQKDLN 240

Query: 241 LALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKLA 292
           LALQSAKALALNLPNTATCQELFNTC ANGGS+LDHS+LVQALELMANHK++
Sbjct: 241 LALQSAKALALNLPNTATCQELFNTCVANGGSELDHSSLVQALELMANHKIS 292


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: 413
Number of extensions: 4
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: 292
Length adjustment: 26
Effective length of query: 266
Effective length of database: 266
Effective search space:    70756
Effective search space used:    70756
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 BWI76_RS07000 BWI76_RS07000 (2-hydroxy-3-oxopropionate 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.18373.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-147  474.1   4.5   8.5e-147  474.0   4.5    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS07000  BWI76_RS07000 2-hydroxy-3-oxopro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS07000  BWI76_RS07000 2-hydroxy-3-oxopropionate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.0   4.5  8.5e-147  8.5e-147       1     291 []       2     291 ..       2     291 .. 1.00

  Alignments for each domain:
  == domain 1  score: 474.0 bits;  conditional E-value: 8.5e-147
                               TIGR01505   1 kvgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqvee 71 
                                             k+gfiGlGimG+Pm+  l+kaG+ l+v+t++ ++++ell  Ga+   ta++v+e++++i++mvPd+Pqv +
  lcl|FitnessBrowser__Koxy:BWI76_RS07000   2 KLGFIGLGIMGTPMALRLAKAGHALHVTTIG-PVAEELLKQGAQHLATAEQVAEQSEIIFIMVPDTPQVAD 71 
                                             89*****************************.9************************************** PP

                               TIGR01505  72 valGenGileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtlsimvGGdkavf 142
                                             v++Ge+G+ +aa+kGk++vdmssi+P+e+k++a++v+++G d+ldaPvsGGe+ga+egtlsimvGGd+ vf
  lcl|FitnessBrowser__Koxy:BWI76_RS07000  72 VLFGEHGCAKAALKGKTIVDMSSISPIETKRFAQQVRDLGADYLDAPVSGGEIGAREGTLSIMVGGDENVF 142
                                             *********************************************************************** PP

                               TIGR01505 143 dkvkpllealgksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGlagstv 213
                                              +vkpl+++lgk+i+lvG+nG+Gqt+kvanq+ivalnieavsealv+a+kaG+dp +v+qal+GG+a+s++
  lcl|FitnessBrowser__Koxy:BWI76_RS07000 143 ARVKPLFDILGKNITLVGGNGDGQTCKVANQIIVALNIEAVSEALVFASKAGADPARVRQALMGGFASSRI 213
                                             *********************************************************************** PP

                               TIGR01505 214 leakkerlldrdfkPGfridlhqkdlalaldaakavgaalPvtavvaellaalradGdgtldhsalvrale 284
                                             le+++er+l+r+f+PGf+i lhqkdl+lal++aka++++lP+ta+++el++++ a+G+++ldhs+lv+ale
  lcl|FitnessBrowser__Koxy:BWI76_RS07000 214 LEVHGERMLNRTFNPGFKISLHQKDLNLALQSAKALALNLPNTATCQELFNTCVANGGSELDHSSLVQALE 284
                                             *********************************************************************** PP

                               TIGR01505 285 klakdkv 291
                                             ++a++k+
  lcl|FitnessBrowser__Koxy:BWI76_RS07000 285 LMANHKI 291
                                             ****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (291 nodes)
Target sequences:                          1  (292 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: 10.98
//
[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