Alignments for a candidate for galE in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Pseudomonas fluorescens FW300-N2E3

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate AO353_21135 AO353_21135 UDP-galactose-4-epimerase

Query= curated2:Q9KDV3
         (334 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21135
          Length = 325

 Score =  347 bits (890), Expect = e-100
 Identities = 167/323 (51%), Positives = 214/323 (66%)

Query: 1   MAILVTGGAGYIGSHTVLFLLEQGEQVIVLDNLQKGHAGALSDVTFYHGDIRDDQLLDTI 60
           M  LV GGAGYIGSH V  LL  G + +V DN   GH GAL        DI D Q LD +
Sbjct: 1   MKFLVVGGAGYIGSHMVKQLLRAGHEPVVADNFSTGHRGALMGGRLVELDIADAQALDVL 60

Query: 61  FTTHSIDTVIHFAANSLVGESVKQPIEYYENNVIGTHTLLKKMLEHDVKKIVFSSTAATY 120
           F     D V HFA+ + VGESV +P +YY+NN+ GT TLL+ ++   VK  +FSS+AA Y
Sbjct: 61  FAGQHFDAVFHFASFTQVGESVTEPAKYYQNNLAGTLTLLQAVVRAGVKNFIFSSSAAIY 120

Query: 121 GEPVQIPIQESDPTIPTNPYGETKLAIEKMFHWCQEAYGLQYVCLRYFNAAGADPNGRIG 180
           G+PV +PI E  P    NPYG +K  +E+M      AYGL+ VCLRYFNAAGADP G++G
Sbjct: 121 GDPVYVPIDEEHPKAAINPYGRSKWMVEQMLEDFDRAYGLKSVCLRYFNAAGADPEGQLG 180

Query: 181 EDHSPESHLIPIVLQVALGQRERVAIFGDDYQTEDGSCIRDYIHVMDLANAHYLACEHLR 240
           E   PE+HL+P++LQ A G+R  + ++G DY T DG+CIRDYIHV+DL  AH LA  +L 
Sbjct: 181 ERREPETHLLPLILQAASGRRTTITVYGRDYDTPDGTCIRDYIHVVDLVAAHALAVNYLL 240

Query: 241 KDGQSGSFNLGNGKGFSVKEVIEVCRQVTGHPIPAEIAPRRSGDPASLIASSEKAQTILG 300
             G S + NLGNG+GFSV++VI+  R VTG  I    APRR GDP  L+A    A T+LG
Sbjct: 241 AGGASTALNLGNGQGFSVQQVIDTARAVTGQGISVSEAPRRVGDPPRLVADPRMANTLLG 300

Query: 301 WEPKYPSLETMVEHAWNWHKEHP 323
           W+P+Y SLE +V HAW+W +++P
Sbjct: 301 WQPQYASLEQIVAHAWSWEQKYP 323


Lambda     K      H
   0.317    0.135    0.411 

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: 372
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: 334
Length of database: 325
Length adjustment: 28
Effective length of query: 306
Effective length of database: 297
Effective search space:    90882
Effective search space used:    90882
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: 49 (23.5 bits)

Align candidate AO353_21135 AO353_21135 (UDP-galactose-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.7658.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.7e-134  433.8   0.0   2.1e-134  433.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21135  AO353_21135 UDP-galactose-4-epim


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_21135  AO353_21135 UDP-galactose-4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  433.5   0.0  2.1e-134  2.1e-134       2     328 ..       3     322 ..       2     324 .. 0.99

  Alignments for each domain:
  == domain 1  score: 433.5 bits;  conditional E-value: 2.1e-134
                                     TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavl 66 
                                                    Lv+GgaGyiGsh+v+qll++g+e vv Dn s+g++ al  ++      lve d+ad+++l+ ++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21135   3 FLVVGGAGYIGSHMVKQLLRAGHEPVVADNFSTGHRGALMGGR------LVELDIADAQALDVLF 61 
                                                   79****************************************9......**************** PP

                                     TIGR01179  67 eeekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekv 131
                                                   + +++dav Hfa++++vgEsv+eP+kYY+nn+ +tl+Ll+a+++agvk++iFsssaa+Yg++  v
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21135  62 AGQHFDAVFHFASFTQVGESVTEPAKYYQNNLAGTLTLLQAVVRAGVKNFIFSSSAAIYGDPVYV 126
                                                   ***************************************************************** PP

                                     TIGR01179 132 pisEesplnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathli 196
                                                   pi Ee+p ++inpYGrsk mvE++l+d+ +a ++lk v LRYFn+aGAd+eg++Ge+ +++thl+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21135 127 PIDEEHPKAAINPYGRSKWMVEQMLEDFDRA-YGLKSVCLRYFNAAGADPEGQLGERREPETHLL 190
                                                   *******************************.********************************* PP

                                     TIGR01179 197 klvaevavgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqg 261
                                                   +l++++a+g+r +++++G dy+t+DGtc+RDyiHv Dl +aH  a+++l +gg s+++nlG+gqg
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21135 191 PLILQAASGRRTTITVYGRDYDTPDGTCIRDYIHVVDLVAAHALAVNYLLAGGASTALNLGNGQG 255
                                                   ***************************************************************** PP

                                     TIGR01179 262 fsvkevieavkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWek 326
                                                   fsv++vi+++++v+g+ i+v++a+rR GDp++lvad+  +++ lgw+p+y  Le+i++ aw+We+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21135 256 FSVQQVIDTARAVTGQGISVSEAPRRVGDPPRLVADPRMANTLLGWQPQYASLEQIVAHAWSWEQ 320
                                                   ****************************************************************9 PP

                                     TIGR01179 327 kl 328
                                                   k 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21135 321 KY 322
                                                   86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (325 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: 10.01
//
[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