Alignments for a candidate for galE in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Caulobacter crescentus NA1000

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate CCNA_02466 CCNA_02466 UDP-glucose 4-epimerase

Query= curated2:Q59745
         (327 letters)



>FitnessBrowser__Caulo:CCNA_02466
          Length = 327

 Score =  432 bits (1112), Expect = e-126
 Identities = 206/318 (64%), Positives = 247/318 (77%)

Query: 4   ETVLVVGGAGYIGSHTCLDLANKGYRPVVFDNFSNGHREFVRWGPAEEGDIRDRARLDEV 63
           +TVLV GGAGY+GSH CL LA  G+RPVV+D+ SNGHRE V+WGP E GDIRD ARLD V
Sbjct: 2   QTVLVAGGAGYVGSHCCLALAAAGFRPVVYDDLSNGHREHVQWGPLEVGDIRDGARLDAV 61

Query: 64  LAKHKPAAILHFAALIEVGESVKDPVSFYENNVIGTLTLLSAAQAAGINAFVFSSTCATY 123
            A H P A+LHFAA IEVGESVK+P +F++NNV GT+TL+ AA+ AG+NA VFSSTCAT+
Sbjct: 62  FAAHAPVAVLHFAARIEVGESVKNPGAFFDNNVGGTITLIEAARRAGVNAMVFSSTCATF 121

Query: 124 GLPQSVPLDETHRQVPINPYGRTKYIVEQALADYDQYGSLRSVVLRYFNAAGADFEGRIG 183
           G P  +P+ E H Q P+NPYGR+K +VEQALADYD+Y   +S V+RYFNAAGAD EGRIG
Sbjct: 122 GDPVHLPMAEDHPQAPLNPYGRSKLMVEQALADYDRYVGFKSAVMRYFNAAGADPEGRIG 181

Query: 184 EWHQPETHAIPLAIDAALGRRQGFKVFGSDYETRDGTCVRDYIHVLDLADAHVRAVEYLL 243
           EWH+PETHAIPLAI  ALG+R  F +FG DY+TRDGT VRDYIHVLDLADAHV A+  LL
Sbjct: 182 EWHEPETHAIPLAIQVALGQRSHFTIFGDDYDTRDGTAVRDYIHVLDLADAHVSALRRLL 241

Query: 244 KGGDSVALNLGTGTGTTVKELLGAIEEVSNRPFPVEYIGRREGDSHTLVANNDKARDVLG 303
            GG S + NLGTGTGTTV+EL+  +  V+ +P PV+   RR GD+  LV +N +AR+ LG
Sbjct: 242 AGGSSDSYNLGTGTGTTVRELVDGVGRVTGKPLPVQMAPRRAGDAPVLVGDNTRAREHLG 301

Query: 304 WVPQYDLSEIIRSAWDWH 321
           W P  DL   + SAW WH
Sbjct: 302 WKPSRDLDATLSSAWRWH 319


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: 418
Number of extensions: 16
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: 327
Length adjustment: 28
Effective length of query: 299
Effective length of database: 299
Effective search space:    89401
Effective search space used:    89401
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 CCNA_02466 CCNA_02466 (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.6269.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-127  410.7   0.0   2.2e-127  410.4   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02466  CCNA_02466 UDP-glucose 4-epimera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02466  CCNA_02466 UDP-glucose 4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.4   0.0  2.2e-127  2.2e-127       2     328 ..       4     322 ..       3     325 .. 0.99

  Alignments for each domain:
  == domain 1  score: 410.4 bits;  conditional E-value: 2.2e-127
                             TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidav 74 
                                           +Lv+GgaGy+Gsh + +l ++g++ vv+D+ls+g++e+++++       l  gd++d ++l+av++++++ av
  lcl|FitnessBrowser__Caulo:CCNA_02466   4 VLVAGGAGYVGSHCCLALAAAGFRPVVYDDLSNGHREHVQWGP------LEVGDIRDGARLDAVFAAHAPVAV 70 
                                           8******************************************......999********************* PP

                             TIGR01179  75 iHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGr 147
                                           +Hfaa+i+vgEsvk+P  +++nnv +t++L+ea ++agv+ ++Fss++a++g++ ++p+ E++p++p npYGr
  lcl|FitnessBrowser__Caulo:CCNA_02466  71 LHFAARIEVGESVKNPGAFFDNNVGGTITLIEAARRAGVNAMVFSSTCATFGDPVHLPMAEDHPQAPLNPYGR 143
                                           ************************************************************************* PP

                             TIGR01179 148 sklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptk 220
                                           sklmvE+ l d+ +   ++k +++RYFn+aGAd+eg+iGe ++++th i+l+++va+g+r++++ifG+dy+t+
  lcl|FitnessBrowser__Caulo:CCNA_02466 144 SKLMVEQALADYDRY-VGFKSAVMRYFNAAGADPEGRIGEWHEPETHAIPLAIQVALGQRSHFTIFGDDYDTR 215
                                           ************999.********************************************************* PP

                             TIGR01179 221 DGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpas 293
                                           DGt+vRDyiHv Dla+aH+ al+ l +gg s+ ynlG+g+g  v+e+++ v +v+gk+++v++a+rRaGD ++
  lcl|FitnessBrowser__Caulo:CCNA_02466 216 DGTAVRDYIHVLDLADAHVSALRRLLAGGSSDSYNLGTGTGTTVRELVDGVGRVTGKPLPVQMAPRRAGDAPV 288
                                           ************************************************************************* PP

                             TIGR01179 294 lvadaskikrelgwkpkyddLeeiiksawdWekkl 328
                                           lv+d+ +++++lgwkp++d L+  ++saw+W++ +
  lcl|FitnessBrowser__Caulo:CCNA_02466 289 LVGDNTRAREHLGWKPSRD-LDATLSSAWRWHQAQ 322
                                           ******************9.***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (327 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: 11.21
//
[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