Alignments for a candidate for galE in Flavobacterium beibuense F44-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Flavobacterium beibuense F44-8

Align UDP-glucose 4-epimerase; EC 5.1.3.2 (characterized, see rationale)
to candidate WP_035135055.1 Q763_RS13115 UDP-glucose 4-epimerase GalE

Query= uniprot:L0FXG3
         (337 letters)



>NCBI__GCF_000769915.1:WP_035135055.1
          Length = 338

 Score =  358 bits (918), Expect = e-103
 Identities = 174/336 (51%), Positives = 245/336 (72%), Gaps = 3/336 (0%)

Query: 3   QILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILGAPVKYHEGDCND 62
           +IL+TGG G+IGSHT V L N G++ +++D+ SNS+ +VLNG+E I G   ++ + D  +
Sbjct: 2   KILVTGGLGFIGSHTVVELQNEGFDVVVIDDLSNSSLDVLNGIESITGKKPEFEKIDLRE 61

Query: 63  RKFMQAVFEEN-DLQGVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKDIV 121
           ++ ++  F +  D+ G+IHFAASKAVGES + PL YY NNI SL+ LL+ +++    + +
Sbjct: 62  KQAVKDFFVKYPDVTGIIHFAASKAVGESVENPLLYYENNIGSLVYLLQELQKKQEFNFI 121

Query: 122 FSSSCTVYGQPDKLPVKETTPRKDAESPYGNTKKICEDILTDHVKSGAPARVVALRYFNP 181
           FSSSCTVYGQ +K+P+ E  P + A SPYGNTK+I E+I+ D  K       V LRYFNP
Sbjct: 122 FSSSCTVYGQAEKMPITEGAPIQGALSPYGNTKQIGEEIIKDVAKVSG-INSVLLRYFNP 180

Query: 182 IGAHPSSLIGELPLGVPANLIPFVTQTGAGIREKITVFGDDYNTPDGTCIRDYIHVMDLA 241
           +GAHPS  IGELPLGVP NL+PF+TQT  GIRE+++VFG+DY T DGTC+RDYIHV+DLA
Sbjct: 181 VGAHPSVNIGELPLGVPLNLVPFITQTAIGIREQLSVFGNDYPTTDGTCVRDYIHVVDLA 240

Query: 242 DAHVKSIQYLADQPE-NFIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGDIE 300
            AHV ++Q L D+     +++FN+GTG GN+V+EVI AFE+VS + LNY+I  RR+GD+ 
Sbjct: 241 KAHVLALQRLIDKKNAEKVEVFNLGTGKGNSVLEVINAFERVSGQKLNYKIVDRRAGDVA 300

Query: 301 KVWANTDKVSKVLGWTPQFGLEEALRDAWNWQLSLK 336
           + +A+T K + VLGW  +  L++AL  AW W+  ++
Sbjct: 301 EAYADTAKANNVLGWKAELSLDDALASAWKWEQKVR 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: 374
Number of extensions: 15
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: 338
Length adjustment: 28
Effective length of query: 309
Effective length of database: 310
Effective search space:    95790
Effective search space used:    95790
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 WP_035135055.1 Q763_RS13115 (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.2040278.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.5e-127  408.7   0.0   8.4e-127  408.5   0.0    1.0  1  NCBI__GCF_000769915.1:WP_035135055.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000769915.1:WP_035135055.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.5   0.0  8.4e-127  8.4e-127       1     329 [.       2     336 ..       2     338 .] 0.97

  Alignments for each domain:
  == domain 1  score: 408.5 bits;  conditional E-value: 8.4e-127
                             TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleee.k 70 
                                           kiLvtGg G+iGsh+v++l+++g++vvv+D+ls++s ++l+ +e it  + ++ + dl++k+++++++ +  +
  NCBI__GCF_000769915.1:WP_035135055.1   2 KILVTGGLGFIGSHTVVELQNEGFDVVVIDDLSNSSLDVLNGIESITgkKPEFEKIDLREKQAVKDFFVKYpD 74 
                                           79********************************************99999****************987637 PP

                             TIGR01179  71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespln.pi 142
                                           +  +iHfaa++avgEsv++Pl YYenn+ + + Ll+++qk + +++iFsss++vYg+ ek+pi+E +p++ + 
  NCBI__GCF_000769915.1:WP_035135055.1  75 VTGIIHFAASKAVGESVENPLLYYENNIGSLVYLLQELQKKQEFNFIFSSSCTVYGQAEKMPITEGAPIQgAL 147
                                           99******************************************************************9989* PP

                             TIGR01179 143 npYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifG 214
                                           +pYG++k + E+i+kd++k+ ++++ v+LRYFn++GA+++ +iGe + + + +l++ ++++a+g re+l++fG
  NCBI__GCF_000769915.1:WP_035135055.1 148 SPYGNTKQIGEEIIKDVAKV-SGINSVLLRYFNPVGAHPSVNIGELPLGVPlNLVPFITQTAIGIREQLSVFG 219
                                           ********************.**************************************************** PP

                             TIGR01179 215 tdyptkDGtcvRDyiHveDlaeaHlaalealeeg...gesevynlGagqgfsvkevieavkkvsgkdikvela 284
                                           +dypt+DGtcvRDyiHv Dla+aH+ al+ l ++   +++ev+nlG+g+g+sv+evi+a+++vsg+++++++ 
  NCBI__GCF_000769915.1:WP_035135055.1 220 NDYPTTDGTCVRDYIHVVDLAKAHVLALQRLIDKknaEKVEVFNLGTGKGNSVLEVINAFERVSGQKLNYKIV 292
                                           *****************************997653336789******************************** PP

                             TIGR01179 285 drRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklk 329
                                           drRaGD+a+ +ad++k++++lgwk+++  L++ ++saw+We+k +
  NCBI__GCF_000769915.1:WP_035135055.1 293 DRRAGDVAEAYADTAKANNVLGWKAELS-LDDALASAWKWEQKVR 336
                                           ****************************.************9875 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 20.60
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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