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 2-hydroxy-3-oxopropionate reductase; Tartronate semialdehyde reductase; TSAR; EC 1.1.1.60 (characterized)
to candidate BWI76_RS24825 BWI76_RS24825 2-hydroxy-3-oxopropionate reductase

Query= SwissProt::P0ABQ2
         (294 letters)



>FitnessBrowser__Koxy:BWI76_RS24825
          Length = 296

 Score =  556 bits (1432), Expect = e-163
 Identities = 287/294 (97%), Positives = 293/294 (99%)

Query: 1   MKVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVI 60
           MKVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIA+VIAAGAETA++AKAIAEQCDVI
Sbjct: 3   MKVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIAEVIAAGAETAASAKAIAEQCDVI 62

Query: 61  ITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLDAPV 120
           ITMLPNSPHVKEVALGE GIIEGAKPGTVLIDMSSIAPLASREISEALKAKG+DMLDAPV
Sbjct: 63  ITMLPNSPHVKEVALGEGGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGVDMLDAPV 122

Query: 121 SGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGEIGAGNVTKLANQVIVALN 180
           SGGEPKAIDGTLSVMVGGDKAIFDKYY+L+KAMAGSVVHTGEIGAGNVTKLANQVIVALN
Sbjct: 123 SGGEPKAIDGTLSVMVGGDKAIFDKYYELLKAMAGSVVHTGEIGAGNVTKLANQVIVALN 182

Query: 181 IAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDL 240
           IAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDL
Sbjct: 183 IAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDL 242

Query: 241 ANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALACYYEKLAKVEVTR 294
           ANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALACYYEKLAKVEVTR
Sbjct: 243 ANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALACYYEKLAKVEVTR 296


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: 431
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: 294
Length of database: 296
Length adjustment: 26
Effective length of query: 268
Effective length of database: 270
Effective search space:    72360
Effective search space used:    72360
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 BWI76_RS24825 BWI76_RS24825 (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.14606.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   4.6e-158  510.9  12.0   5.2e-158  510.8  12.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS24825  BWI76_RS24825 2-hydroxy-3-oxopro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS24825  BWI76_RS24825 2-hydroxy-3-oxopropionate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  510.8  12.0  5.2e-158  5.2e-158       1     291 []       4     294 ..       4     294 .. 1.00

  Alignments for each domain:
  == domain 1  score: 510.8 bits;  conditional E-value: 5.2e-158
                               TIGR01505   1 kvgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqvee 71 
                                             kvgfiGlGimGkPmsknllkaGy+lvva++++ea++e++aaGae+a +ak+++e++dvi+tm+P+sP+v+e
  lcl|FitnessBrowser__Koxy:BWI76_RS24825   4 KVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIAEVIAAGAETAASAKAIAEQCDVIITMLPNSPHVKE 74 
                                             8********************************************************************** PP

                               TIGR01505  72 valGenGileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtlsimvGGdkavf 142
                                             valGe Gi+e+ak+G+vl+dmssiaPl+s+e+++a+k+kG+d+ldaPvsGGe++ai+gtls+mvGGdka+f
  lcl|FitnessBrowser__Koxy:BWI76_RS24825  75 VALGEGGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGVDMLDAPVSGGEPKAIDGTLSVMVGGDKAIF 145
                                             *********************************************************************** PP

                               TIGR01505 143 dkvkpllealgksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGlagstv 213
                                             dk+++ll+a+++s+v++Ge+GaG+++k+anqvivalni+a+seal+la+kaGv+p++v+qa+rGGlagstv
  lcl|FitnessBrowser__Koxy:BWI76_RS24825 146 DKYYELLKAMAGSVVHTGEIGAGNVTKLANQVIVALNIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTV 216
                                             *********************************************************************** PP

                               TIGR01505 214 leakkerlldrdfkPGfridlhqkdlalaldaakavgaalPvtavvaellaalradGdgtldhsalvrale 284
                                             l+ak+++++dr+fkPGfridlh+kdla+ald++++vga+lP+ta+v+e+++alradG gt+dhsal++++e
  lcl|FitnessBrowser__Koxy:BWI76_RS24825 217 LDAKAPMVMDRNFKPGFRIDLHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALACYYE 287
                                             *********************************************************************** PP

                               TIGR01505 285 klakdkv 291
                                             klak++v
  lcl|FitnessBrowser__Koxy:BWI76_RS24825 288 KLAKVEV 294
                                             ****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (291 nodes)
Target sequences:                          1  (296 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: 00:00:00.01
# Mc/sec: 7.31
//
[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