Alignments for a candidate for galE in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Sinorhizobium meliloti 1021

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate SM_b20942 SM_b20942 UDP glucose 4-epimerase

Query= curated2:Q59745
         (327 letters)



>FitnessBrowser__Smeli:SM_b20942
          Length = 328

 Score =  548 bits (1411), Expect = e-161
 Identities = 262/326 (80%), Positives = 291/326 (89%)

Query: 1   MAGETVLVVGGAGYIGSHTCLDLANKGYRPVVFDNFSNGHREFVRWGPAEEGDIRDRARL 60
           M    +LVVGGAGYIGSHTCL LA KGY+PVV+DN SNGH EFV+WG  E+GDIRDR RL
Sbjct: 1   MQNNNILVVGGAGYIGSHTCLQLAAKGYQPVVYDNLSNGHEEFVKWGVLEKGDIRDRQRL 60

Query: 61  DEVLAKHKPAAILHFAALIEVGESVKDPVSFYENNVIGTLTLLSAAQAAGINAFVFSSTC 120
           DEVLA+HKP AILHFAA+IEVGESVKDP +FY+NNVIGTLTLLSAA AAGI+AFVFSSTC
Sbjct: 61  DEVLARHKPRAILHFAAMIEVGESVKDPAAFYDNNVIGTLTLLSAALAAGIDAFVFSSTC 120

Query: 121 ATYGLPQSVPLDETHRQVPINPYGRTKYIVEQALADYDQYGSLRSVVLRYFNAAGADFEG 180
           ATYGLP SVP+DE+H+Q PINPYGRTK+I EQAL DY  Y  LRSV+LRYFNAAGADFEG
Sbjct: 121 ATYGLPDSVPMDESHKQAPINPYGRTKWICEQALKDYGLYKGLRSVILRYFNAAGADFEG 180

Query: 181 RIGEWHQPETHAIPLAIDAALGRRQGFKVFGSDYETRDGTCVRDYIHVLDLADAHVRAVE 240
           RIGEWH+PETHAIPLAIDAALGRR+GFKVFG+DY+TRDGTCVRDYIHVLDLADAHVRAV+
Sbjct: 181 RIGEWHEPETHAIPLAIDAALGRREGFKVFGTDYDTRDGTCVRDYIHVLDLADAHVRAVD 240

Query: 241 YLLKGGDSVALNLGTGTGTTVKELLGAIEEVSNRPFPVEYIGRREGDSHTLVANNDKARD 300
           YLL+GG+SVALNLGTGTGTTVKELL AIE+V+ RPF + Y  RREGDS TLVANNDKAR 
Sbjct: 241 YLLEGGESVALNLGTGTGTTVKELLDAIEKVAKRPFNIGYAERREGDSTTLVANNDKARQ 300

Query: 301 VLGWVPQYDLSEIIRSAWDWHAKSNQ 326
           VLGW PQYDL+ I  SAW+WH++ NQ
Sbjct: 301 VLGWEPQYDLAAITESAWNWHSRRNQ 326


Lambda     K      H
   0.319    0.137    0.415 

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: 494
Number of extensions: 8
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: 327
Length of database: 328
Length adjustment: 28
Effective length of query: 299
Effective length of database: 300
Effective search space:    89700
Effective search space used:    89700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate SM_b20942 SM_b20942 (UDP glucose 4-epimerase)
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))

# 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/TIGR01179.hmm
# target sequence database:        /tmp/gapView.28660.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01179  [M=332]
Accession:   TIGR01179
Description: galE: UDP-glucose 4-epimerase GalE
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   8.5e-133  428.2   0.0   9.5e-133  428.1   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SM_b20942  SM_b20942 UDP glucose 4-epimeras


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b20942  SM_b20942 UDP glucose 4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.1   0.0  9.5e-133  9.5e-133       1     330 [.       5     326 ..       5     328 .] 0.99

  Alignments for each domain:
  == domain 1  score: 428.1 bits;  conditional E-value: 9.5e-133
                            TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidav 74 
                                          +iLv+GgaGyiGsh++ ql +kg++ vv+Dnls+g++e++k++       l +gd++d+++l++vl+++k+ a+
  lcl|FitnessBrowser__Smeli:SM_b20942   5 NILVVGGAGYIGSHTCLQLAAKGYQPVVYDNLSNGHEEFVKWGV------LEKGDIRDRQRLDEVLARHKPRAI 72 
                                          59*****************************************9......99********************** PP

                            TIGR01179  75 iHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrs 148
                                          +Hfaa+i+vgEsvk+P+ +Y+nnv +tl+Ll+a  +ag+  ++Fss++a+Yg +++vp+ E+++++pinpYGr+
  lcl|FitnessBrowser__Smeli:SM_b20942  73 LHFAAMIEVGESVKDPAAFYDNNVIGTLTLLSAALAAGIDAFVFSSTCATYGLPDSVPMDESHKQAPINPYGRT 146
                                          ************************************************************************** PP

                            TIGR01179 149 klmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptkDG 222
                                          k + E+ lkd+    k+l+ viLRYFn+aGAd eg+iGe ++++th i+l++++a+g+re +++fGtdy+t+DG
  lcl|FitnessBrowser__Smeli:SM_b20942 147 KWICEQALKDYGLY-KGLRSVILRYFNAAGADFEGRIGEWHEPETHAIPLAIDAALGRREGFKVFGTDYDTRDG 219
                                          ***********888.*********************************************************** PP

                            TIGR01179 223 tcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslva 296
                                          tcvRDyiHv Dla+aH++a+++l egges ++nlG+g+g  vke+++a++kv+ +++++  a+rR+GD ++lva
  lcl|FitnessBrowser__Smeli:SM_b20942 220 TCVRDYIHVLDLADAHVRAVDYLLEGGESVALNLGTGTGTTVKELLDAIEKVAKRPFNIGYAERREGDSTTLVA 293
                                          ************************************************************************** PP

                            TIGR01179 297 daskikrelgwkpkyddLeeiiksawdWekklke 330
                                          +++k++++lgw+p+yd L+ i +saw+W++++++
  lcl|FitnessBrowser__Smeli:SM_b20942 294 NNDKARQVLGWEPQYD-LAAITESAWNWHSRRNQ 326
                                          ****************.*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (328 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.37
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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