Alignments for a candidate for galE in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Pseudovibrio axinellae Ad2

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_074882175.1 PsAD2_RS10675 UDP-glucose 4-epimerase GalE

Query= curated2:Q59083
         (348 letters)



>NCBI__GCF_001623255.1:WP_074882175.1
          Length = 329

 Score =  360 bits (923), Expect = e-104
 Identities = 185/322 (57%), Positives = 223/322 (69%)

Query: 11  VLVTGGAGYIGSHVLHALTDAGIPAVTIDDLSAGRREAIPAAVPLVEGDIGSAELLDRVM 70
           +LVTGGAGYIGSH+   L DAG   V ID+LS G   AIP +V L EGDI   +LL  + 
Sbjct: 3   ILVTGGAGYIGSHMAWCLHDAGEDFVVIDNLSTGFEWAIPQSVKLYEGDITDEKLLQTIF 62

Query: 71  RDHRVDAVMHFAGSIVVPESVVKPLDYYRNNTANSLTLLGACLRAGIDKVVFSSTAAVYG 130
            +H + AV+HFAGSI+VPESV  PL YY NNTA S TL+ AC++  I   +FSSTAAVYG
Sbjct: 63  HNHDITAVIHFAGSIIVPESVSNPLKYYNNNTAASRTLIEACVKNNIKHFIFSSTAAVYG 122

Query: 131 APESVPIREDAPTVPINPYGASKLMTEQMLRDAGAAHGLRSVILRYFNVAGADPAGRTGQ 190
            P+ +P+ EDAP  P++PYG SKLMTE MLRD  AAH  +   LRYFNVAGADP GRTGQ
Sbjct: 123 DPKVIPVSEDAPLSPLSPYGTSKLMTELMLRDTAAAHDFQYTALRYFNVAGADPEGRTGQ 182

Query: 191 ATPVATHLIKVACQALLGRRPPLAIFGTDYDTPDGTCIRDYIHVSDLADAHVLALLHLRR 250
           +T  ATHLIKVAC+A LG+R  L IFG D+DTPD T IRDYIHVSDLA AH LAL  LR 
Sbjct: 183 STRNATHLIKVACEAALGKRTHLGIFGADFDTPDKTGIRDYIHVSDLASAHYLALKRLRE 242

Query: 251 GGGSLLMNCGYGRGASVREVVRTLEEVSGEQVPATFADRRPGDPPQLVAGADRIREQLGW 310
           GG S++MN GYG G SV +V+  ++ VS          RR GD P++VA   +I   L W
Sbjct: 243 GGESIVMNAGYGDGYSVLQVIDAVKAVSEVDFEVKTEPRRAGDSPKVVADNSKIMSNLDW 302

Query: 311 VPKHDRLDGIVRSALSWERSLE 332
            P+ D L  I+R AL+WE+ L+
Sbjct: 303 KPQFDDLPTIIRHALNWEKKLQ 324


Lambda     K      H
   0.319    0.136    0.401 

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: 352
Number of extensions: 10
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: 348
Length of database: 329
Length adjustment: 28
Effective length of query: 320
Effective length of database: 301
Effective search space:    96320
Effective search space used:    96320
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: 49 (23.5 bits)

Align candidate WP_074882175.1 PsAD2_RS10675 (UDP-glucose 4-epimerase GalE)
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.2241196.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.5e-137  442.6   0.0   4.1e-137  442.4   0.0    1.0  1  NCBI__GCF_001623255.1:WP_074882175.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001623255.1:WP_074882175.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.4   0.0  4.1e-137  4.1e-137       2     329 ..       3     324 ..       2     327 .. 0.99

  Alignments for each domain:
  == domain 1  score: 442.4 bits;  conditional E-value: 4.1e-137
                             TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidav 74 
                                           iLvtGgaGyiGsh++  l ++g + vv+Dnls+g+++a+++       kl+egd++d++ l++++++++i av
  NCBI__GCF_001623255.1:WP_074882175.1   3 ILVTGGAGYIGSHMAWCLHDAGEDFVVIDNLSTGFEWAIPQSV-----KLYEGDITDEKLLQTIFHNHDITAV 70 
                                           9**************************************9987.....6************************ PP

                             TIGR01179  75 iHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGr 147
                                           iHfa++i v+Esv++PlkYY+nn+ ++ +L+ea++k ++k++iFss+aavYg+++ +p+sE++pl+p +pYG+
  NCBI__GCF_001623255.1:WP_074882175.1  71 IHFAGSIIVPESVSNPLKYYNNNTAASRTLIEACVKNNIKHFIFSSTAAVYGDPKVIPVSEDAPLSPLSPYGT 143
                                           ************************************************************************* PP

                             TIGR01179 148 sklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptk 220
                                           sklm+E +l+d++ a +++++++LRYFnvaGAd+eg+ G++++nathlik+++e+a+gkr +l ifG d++t+
  NCBI__GCF_001623255.1:WP_074882175.1 144 SKLMTELMLRDTAAA-HDFQYTALRYFNVAGADPEGRTGQSTRNATHLIKVACEAALGKRTHLGIFGADFDTP 215
                                           ************999.********************************************************* PP

                             TIGR01179 221 DGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpas 293
                                           D t++RDyiHv+Dla+aH  al+ l egges v n G+g g+sv++vi+avk+vs +d++v+ ++rRaGD ++
  NCBI__GCF_001623255.1:WP_074882175.1 216 DKTGIRDYIHVSDLASAHYLALKRLREGGESIVMNAGYGDGYSVLQVIDAVKAVSEVDFEVKTEPRRAGDSPK 288
                                           ************************************************************************* PP

                             TIGR01179 294 lvadaskikrelgwkpkyddLeeiiksawdWekklk 329
                                           +vad+ski ++l+wkp++ddL +ii+ a++Wekkl+
  NCBI__GCF_001623255.1:WP_074882175.1 289 VVADNSKIMSNLDWKPQFDDLPTIIRHALNWEKKLQ 324
                                           ********************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (329 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: 00:00:00.00
# Mc/sec: 12.55
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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