Alignments for a candidate for galE in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Pedobacter sp. GW460-11-11-14-LB5

Align UDP-glucose 4-epimerase; EC 5.1.3.2 (characterized, see rationale)
to candidate CA265_RS25430 CA265_RS25430 UDP-glucose 4-epimerase GalE

Query= uniprot:L0FXG3
         (337 letters)



>FitnessBrowser__Pedo557:CA265_RS25430
          Length = 340

 Score =  364 bits (935), Expect = e-105
 Identities = 183/338 (54%), Positives = 238/338 (70%), Gaps = 4/338 (1%)

Query: 1   MQQILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILGAPVKYHEGDC 60
           M +IL+TGG GYIGSHTAV L NAGYE +IVDN SNSN ++L  L  I G    +HE D 
Sbjct: 1   MAKILVTGGTGYIGSHTAVELHNAGYEVVIVDNLSNSNIKILTQLHAITGKWFDFHEIDL 60

Query: 61  NDRKFMQAVFEEN-DLQGVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKD 119
            D + +Q   E + D+ G+IHFAASKAVGES + PL YY NN   LI LL +  +    +
Sbjct: 61  QDDRAVQEFAENHTDIDGIIHFAASKAVGESVEQPLKYYKNNFYGLINLLTSFNR--KIN 118

Query: 120 IVFSSSCTVYGQPDKLPVKETTPRKDAESPYGNTKKICEDILTDHVKSGAPARVVALRYF 179
            VFSSSCTVYGQP+ LPV E  P + AESPYGNTK+I E+IL +         ++ALRYF
Sbjct: 119 FVFSSSCTVYGQPETLPVTEAAPVQKAESPYGNTKQIAEEILAETAAVTPALNIIALRYF 178

Query: 180 NPIGAHPSSLIGELPLGVPANLIPFVTQTGAGIREKITVFGDDYNTPDGTCIRDYIHVMD 239
           NP+GAH ++LIGELP GVPANL+PF+TQ+  G R  ITV+GDDY+TPDG+ IRDYIHV+D
Sbjct: 179 NPVGAHETALIGELPNGVPANLVPFITQSAIGKRGPITVYGDDYDTPDGSAIRDYIHVVD 238

Query: 240 LADAHVKSIQYLAD-QPENFIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGD 298
           LA AHV +I+ L +  P    D+FN+GTG G++V+E+I AFEKV+ + L+Y+IGPRR+GD
Sbjct: 239 LAKAHVAAIKKLEEGNPNGNYDVFNIGTGKGSSVLEIIAAFEKVNGEKLDYKIGPRRAGD 298

Query: 299 IEKVWANTDKVSKVLGWTPQFGLEEALRDAWNWQLSLK 336
           I +++ +  K +  LGW     + E +R AW W+  +K
Sbjct: 299 IVQIYGDVQKSNNELGWKANLDINEMMRSAWEWEKYIK 336


Lambda     K      H
   0.316    0.136    0.403 

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: 398
Number of extensions: 18
Number of successful extensions: 4
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: 337
Length of database: 340
Length adjustment: 28
Effective length of query: 309
Effective length of database: 312
Effective search space:    96408
Effective search space used:    96408
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate CA265_RS25430 CA265_RS25430 (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.10641.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   5.9e-123  395.9   0.1   6.6e-123  395.7   0.1    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS25430  CA265_RS25430 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS25430  CA265_RS25430 UDP-glucose 4-epimerase GalE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.7   0.1  6.6e-123  6.6e-123       1     329 [.       3     336 ..       3     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 395.7 bits;  conditional E-value: 6.6e-123
                                  TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavl 66 
                                                kiLvtGg+GyiGsh++++l ++g+evv++Dnls+++ ++l++l+ it   + + e dl+d ++++++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS25430   3 KILVTGGTGYIGSHTAVELHNAGYEVVIVDNLSNSNIKILTQLHAITgkWFDFHEIDLQDDRAVQEFA 70 
                                                79********************************************998899**************99 PP

                                  TIGR01179  67 e.eekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpi 133
                                                e +++id +iHfaa++avgEsv++PlkYY+nn  + ++Ll + ++    +++Fsss++vYg++e++p+
  lcl|FitnessBrowser__Pedo557:CA265_RS25430  71 EnHTDIDGIIHFAASKAVGESVEQPLKYYKNNFYGLINLLTSFNR--KINFVFSSSCTVYGQPETLPV 136
                                                83458***********************************99976..579****************** PP

                                  TIGR01179 134 sEespln.pinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklv 199
                                                +E++p++ +++pYG++k ++E+il +++ + ++l++++LRYFn++GA+e   iGe +++ + +l++ +
  lcl|FitnessBrowser__Pedo557:CA265_RS25430 137 TEAAPVQkAESPYGNTKQIAEEILAETAAVTPALNIIALRYFNPVGAHETALIGELPNGVPaNLVPFI 204
                                                *****9989*********************************************************** PP

                                  TIGR01179 200 aevavgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeg...gesevynlGagqgfsv 264
                                                ++ a+gkr  ++++G+dy+t+DG ++RDyiHv Dla+aH+aa+++leeg   g+++v+n+G+g+g sv
  lcl|FitnessBrowser__Pedo557:CA265_RS25430 205 TQSAIGKRGPITVYGDDYDTPDGSAIRDYIHVVDLAKAHVAAIKKLEEGnpnGNYDVFNIGTGKGSSV 272
                                                ***********************************************985545899************ PP

                                  TIGR01179 265 kevieavkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklk 329
                                                +e+i a++kv g+++ +++ +rRaGD+ ++++d +k ++elgwk+++d ++e+++saw+Wek +k
  lcl|FitnessBrowser__Pedo557:CA265_RS25430 273 LEIIAAFEKVNGEKLDYKIGPRRAGDIVQIYGDVQKSNNELGWKANLD-INEMMRSAWEWEKYIK 336
                                                ***********************************************9.************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (340 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: 8.62
//
[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