Alignments for a candidate for galE in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Escherichia coli BW25113

Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate 14884 b0759 UDP-galactose-4-epimerase (VIMSS)

Query= BRENDA::P09147
         (338 letters)



>FitnessBrowser__Keio:14884
          Length = 338

 Score =  699 bits (1804), Expect = 0.0
 Identities = 338/338 (100%), Positives = 338/338 (100%)

Query: 1   MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIR 60
           MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIR
Sbjct: 1   MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIR 60

Query: 61  NEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFI 120
           NEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFI
Sbjct: 61  NEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFI 120

Query: 121 FSSSATVYGDQPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNP 180
           FSSSATVYGDQPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNP
Sbjct: 121 FSSSATVYGDQPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNP 180

Query: 181 VGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLA 240
           VGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLA
Sbjct: 181 VGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLA 240

Query: 241 DGHVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYW 300
           DGHVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYW
Sbjct: 241 DGHVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYW 300

Query: 301 ADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD 338
           ADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD
Sbjct: 301 ADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD 338


Lambda     K      H
   0.318    0.136    0.419 

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: 610
Number of extensions: 9
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: 338
Length of database: 338
Length adjustment: 28
Effective length of query: 310
Effective length of database: 310
Effective search space:    96100
Effective search space used:    96100
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 14884 b0759 (UDP-galactose-4-epimerase (VIMSS))
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.5795.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.4e-154  499.8   0.0   1.6e-154  499.7   0.0    1.0  1  lcl|FitnessBrowser__Keio:14884  b0759 UDP-galactose-4-epimerase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14884  b0759 UDP-galactose-4-epimerase (VIMSS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  499.7   0.0  1.6e-154  1.6e-154       1     331 [.       2     335 ..       2     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 499.7 bits;  conditional E-value: 1.6e-154
                       TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeekidaviHf 77 
                                     ++LvtGg+GyiGsh+++qll++g++v++lDnl+++++++l+++e++   + ++vegd+++++ ++++l++++id+viHf
  lcl|FitnessBrowser__Keio:14884   2 RVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGgkHPTFVEGDIRNEALMTEILHDHAIDTVIHF 80 
                                     69*******************************************99989***************************** PP

                       TIGR01179  78 aaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespln.pinpYGrsklmvEri 155
                                     a+l+avgEsv++Pl+YY+nnv++tl+L++am++a+vk++iFsssa+vYg++ k+p+ E++p++ p++pYG+sklmvE+i
  lcl|FitnessBrowser__Keio:14884  81 AGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFIFSSSATVYGDQPKIPYVESFPTGtPQSPYGKSKLMVEQI 159
                                     **************************************************************99*************** PP

                       TIGR01179 156 lkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGtdyptkDGtcvRDyiHveD 233
                                     l+dl+ka++++++++LRYFn++GA+++g++Ge++++++ +l++++a+vavg+r++l+ifG+dypt+DGt+vRDyiHv+D
  lcl|FitnessBrowser__Keio:14884 160 LTDLQKAQPDWSIALLRYFNPVGAHPSGDMGEDPQGIPnNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMD 238
                                     **************************************9**************************************** PP

                       TIGR01179 234 laeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyd 312
                                     la++H+ a+e+l+++ ++++ynlGag g+sv++v++a++k++gk++++++a+rR+GD+++++adask++rel+w+++++
  lcl|FitnessBrowser__Keio:14884 239 LADGHVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYWADASKADRELNWRVTRT 317
                                     ******************************************************************************* PP

                       TIGR01179 313 dLeeiiksawdWekklkeg 331
                                      L+e+ +++w+W++++++g
  lcl|FitnessBrowser__Keio:14884 318 -LDEMAQDTWHWQSRHPQG 335
                                     .***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (338 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: 00:00:00.01
# Mc/sec: 9.09
//
[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