Alignments for a candidate for galE in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Bacteroides thetaiotaomicron VPI-5482

Align UDP-glucose 4-epimerase; EC 5.1.3.2 (characterized, see rationale)
to candidate 350151 BT0623 putative UDP-glucose 4-epimerase (NCBI ptt file)

Query= uniprot:L0FXG3
         (337 letters)



>FitnessBrowser__Btheta:350151
          Length = 344

 Score =  399 bits (1024), Expect = e-116
 Identities = 196/338 (57%), Positives = 256/338 (75%), Gaps = 2/338 (0%)

Query: 2   QQILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILGAPVKYHEGDCN 61
           ++IL+TGG GYIGSHT V L N+GYE II+DN SNS+ +V++ +EK+ G    + + DC 
Sbjct: 3   ERILVTGGTGYIGSHTVVELQNSGYEVIIIDNLSNSSADVVDNIEKVSGIRPAFEKLDCL 62

Query: 62  DRKFMQAVFEE-NDLQGVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKDI 120
           D   + AVF +   ++ +IHFAASKAVGES + PL YY NN+ SLI LLE M + GV+ I
Sbjct: 63  DFAGLDAVFAKYKGIKAIIHFAASKAVGESVEKPLLYYRNNLVSLINLLELMPKHGVEGI 122

Query: 121 VFSSSCTVYGQPDKLPVKETTPRKDAESPYGNTKKICEDILTDHVKSGAPARVVALRYFN 180
           VFSSSCTVYGQPD+LPV E  P K AESPYGNTK+I E+I+ D + SGAP   + LRYFN
Sbjct: 123 VFSSSCTVYGQPDELPVTEKAPIKKAESPYGNTKQINEEIIRDTIASGAPINAILLRYFN 182

Query: 181 PIGAHPSSLIGELPLGVPANLIPFVTQTGAGIREKITVFGDDYNTPDGTCIRDYIHVMDL 240
           PIGAHP++L+GELP GVP NLIP++TQT  GIREK++VFGDDY+TPDG+CIRD+I+V+DL
Sbjct: 183 PIGAHPTALLGELPNGVPQNLIPYLTQTAMGIREKLSVFGDDYDTPDGSCIRDFINVVDL 242

Query: 241 ADAHVKSIQYLADQPE-NFIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGDI 299
           A AHV +I+ + +Q +   +++FN+GTG G +V+E+I  FEK +   LNY+I  RR+GDI
Sbjct: 243 AKAHVIAIRRILEQKQKEKVEVFNIGTGRGVSVLELINGFEKATGVKLNYQIVGRRAGDI 302

Query: 300 EKVWANTDKVSKVLGWTPQFGLEEALRDAWNWQLSLKK 337
           EKVWAN D  ++ LGW     LE+ LR AWNWQL L++
Sbjct: 303 EKVWANPDYANQELGWKAVETLEDTLRSAWNWQLKLRE 340


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: 413
Number of extensions: 12
Number of successful extensions: 3
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: 344
Length adjustment: 28
Effective length of query: 309
Effective length of database: 316
Effective search space:    97644
Effective search space used:    97644
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 350151 BT0623 (putative UDP-glucose 4-epimerase (NCBI ptt file))
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.25000.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   3.1e-124  400.0   0.0   3.6e-124  399.9   0.0    1.0  1  lcl|FitnessBrowser__Btheta:350151  BT0623 putative UDP-glucose 4-ep


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350151  BT0623 putative UDP-glucose 4-epimerase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.9   0.0  3.6e-124  3.6e-124       1     329 [.       4     339 ..       4     342 .. 0.96

  Alignments for each domain:
  == domain 1  score: 399.9 bits;  conditional E-value: 3.6e-124
                          TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeek.ida 73 
                                        +iLvtGg+GyiGsh+v++l+++g+ev+++Dnls++s++++ ++ek++  + ++ + d  d + l+av+++ k i+a
  lcl|FitnessBrowser__Btheta:350151   4 RILVTGGTGYIGSHTVVELQNSGYEVIIIDNLSNSSADVVDNIEKVSgiRPAFEKLDCLDFAGLDAVFAKYKgIKA 79 
                                        69********************************************999999****************986559** PP

                          TIGR01179  74 viHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespln.pinpYGrs 148
                                        +iHfaa++avgEsv++Pl YY+nn+v+ ++Lle+m k+gv+ ++Fsss++vYg+++++p++E++p++ +++pYG++
  lcl|FitnessBrowser__Btheta:350151  80 IIHFAASKAVGESVEKPLLYYRNNLVSLINLLELMPKHGVEGIVFSSSCTVYGQPDELPVTEKAPIKkAESPYGNT 155
                                        *****************************************************************9989******* PP

                          TIGR01179 149 klmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGtdyptkDGt 223
                                        k + E+i++d+  + + ++ ++LRYFn++GA++   +Ge +++ + +li++++++a+g rekl++fG+dy+t+DG 
  lcl|FitnessBrowser__Btheta:350151 156 KQINEEIIRDTIASGAPINAILLRYFNPIGAHPTALLGELPNGVPqNLIPYLTQTAMGIREKLSVFGDDYDTPDGS 231
                                        **************************************************************************** PP

                          TIGR01179 224 cvRDyiHveDlaeaHlaalealeeg...gesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslva 296
                                        c+RD+i v Dla+aH+ a++ + e+   +++ev+n+G+g+g sv+e+i+ ++k++g+++++++  rRaGD+ +++a
  lcl|FitnessBrowser__Btheta:350151 232 CIRDFINVVDLAKAHVIAIRRILEQkqkEKVEVFNIGTGRGVSVLELINGFEKATGVKLNYQIVGRRAGDIEKVWA 307
                                        *******************9765432227899******************************************** PP

                          TIGR01179 297 daskikrelgwkpkyddLeeiiksawdWekklk 329
                                        +++++++elgwk+  + Le+ ++saw+W+ kl+
  lcl|FitnessBrowser__Btheta:350151 308 NPDYANQELGWKAVET-LEDTLRSAWNWQLKLR 339
                                        ************9988.***********98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (344 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 11.84
//
[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