Alignments for a candidate for galE in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Pseudomonas putida KT2440

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate PP_3129 PP_3129 UDP-glucose 4-epimerase

Query= curated2:Q9KDV3
         (334 letters)



>FitnessBrowser__Putida:PP_3129
          Length = 321

 Score =  323 bits (827), Expect = 5e-93
 Identities = 162/323 (50%), Positives = 210/323 (65%), Gaps = 5/323 (1%)

Query: 1   MAILVTGGAGYIGSHTVLFLLEQGEQVIVLDNLQKGHAGALSDVTFYHGDIRDDQLLDTI 60
           M  LV GGAGYIGSH V  LL  G +V+V D +  G       + +   DI D+  LD +
Sbjct: 1   MKYLVVGGAGYIGSHMVKHLLAAGHEVLVADLVSPGPG-----IQWAKLDIADEAALDVL 55

Query: 61  FTTHSIDTVIHFAANSLVGESVKQPIEYYENNVIGTHTLLKKMLEHDVKKIVFSSTAATY 120
           F     D V HFA+   VGESV  P +YY+NNV  T +LL+ M+   ++ +VFSS+AA Y
Sbjct: 56  FGVCRFDAVFHFASFIQVGESVSAPGKYYQNNVAATLSLLQAMVNAGIRHLVFSSSAAVY 115

Query: 121 GEPVQIPIQESDPTIPTNPYGETKLAIEKMFHWCQEAYGLQYVCLRYFNAAGADPNGRIG 180
           G P  +PI E+    P NPYG +K  +E++      AYGL+ V LRYFNAAGADP G++G
Sbjct: 116 GNPQYVPIDEAHTKGPINPYGLSKWMVEQILEDFDRAYGLKSVSLRYFNAAGADPEGQLG 175

Query: 181 EDHSPESHLIPIVLQVALGQRERVAIFGDDYQTEDGSCIRDYIHVMDLANAHYLACEHLR 240
           E H PE+HLIP++LQ A G+RE V +FG DY T DG+CIRDY+HV DLA AH LA ++L 
Sbjct: 176 ERHEPETHLIPLILQAASGRREAVTVFGRDYDTPDGTCIRDYVHVADLAAAHALAVDYLL 235

Query: 241 KDGQSGSFNLGNGKGFSVKEVIEVCRQVTGHPIPAEIAPRRSGDPASLIASSEKAQTILG 300
             G+  +FNLGNG GFSV++VI+  R VTG  I A  A RR+GDP  L+A + KA  +LG
Sbjct: 236 DGGERAAFNLGNGLGFSVQQVIDTARAVTGRQITALDAQRRAGDPPRLVADASKAMQVLG 295

Query: 301 WEPKYPSLETMVEHAWNWHKEHP 323
           W P + SLE +V HAW W  ++P
Sbjct: 296 WRPAFASLEQIVRHAWQWELQYP 318


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: 327
Number of extensions: 9
Number of successful extensions: 2
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: 321
Length adjustment: 28
Effective length of query: 306
Effective length of database: 293
Effective search space:    89658
Effective search space used:    89658
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: 48 (23.1 bits)

Align candidate PP_3129 PP_3129 (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.19790.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-128  414.1   0.0   2.5e-128  413.5   0.0    1.2  1  lcl|FitnessBrowser__Putida:PP_3129  PP_3129 UDP-glucose 4-epimerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3129  PP_3129 UDP-glucose 4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.5   0.0  2.5e-128  2.5e-128       2     327 ..       3     316 ..       2     320 .. 0.98

  Alignments for each domain:
  == domain 1  score: 413.5 bits;  conditional E-value: 2.5e-128
                           TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidaviH 76 
                                          Lv+GgaGyiGsh+v++ll++g+ev+v D +s g    +++ +          d+ad+++l+ ++   ++dav H
  lcl|FitnessBrowser__Putida:PP_3129   3 YLVVGGAGYIGSHMVKHLLAAGHEVLVADLVSPGPG--IQWAK---------LDIADEAALDVLFGVCRFDAVFH 66 
                                         59***************************9999964..55555.........79********************* PP

                           TIGR01179  77 faaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrsklm 151
                                         fa++i+vgEsv++P kYY+nnv +tl+Ll+am++ag+++l+FsssaavYg+++ vpi E+++ +pinpYG sk m
  lcl|FitnessBrowser__Putida:PP_3129  67 FASFIQVGESVSAPGKYYQNNVAATLSLLQAMVNAGIRHLVFSSSAAVYGNPQYVPIDEAHTKGPINPYGLSKWM 141
                                         *************************************************************************** PP

                           TIGR01179 152 vErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptkDGtcvR 226
                                         vE+il+d+ +a ++lk v+LRYFn+aGAd+eg++Ge+++++thli+l++++a+g+re++++fG dy+t+DGtc+R
  lcl|FitnessBrowser__Putida:PP_3129 142 VEQILEDFDRA-YGLKSVSLRYFNAAGADPEGQLGERHEPETHLIPLILQAASGRREAVTVFGRDYDTPDGTCIR 215
                                         ***********.*************************************************************** PP

                           TIGR01179 227 DyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadaski 301
                                         Dy+Hv Dla+aH  a+++l +gge +++nlG+g gfsv++vi+++++v+g++i++  a+rRaGDp++lvadask+
  lcl|FitnessBrowser__Putida:PP_3129 216 DYVHVADLAAAHALAVDYLLDGGERAAFNLGNGLGFSVQQVIDTARAVTGRQITALDAQRRAGDPPRLVADASKA 290
                                         *************************************************************************** PP

                           TIGR01179 302 krelgwkpkyddLeeiiksawdWekk 327
                                          ++lgw+p +  Le+i++ aw+We +
  lcl|FitnessBrowser__Putida:PP_3129 291 MQVLGWRPAFASLEQIVRHAWQWELQ 316
                                         ***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (321 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: 10.72
//
[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