Alignments for a candidate for galE in Pontibacter ramchanderi LP43

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Pontibacter ramchanderi LP43

Align UDP-glucose 4-epimerase; EC 5.1.3.2 (characterized, see rationale)
to candidate WP_101444364.1 BD749_RS10905 UDP-glucose 4-epimerase GalE

Query= uniprot:L0FXG3
         (337 letters)



>NCBI__GCF_002846395.1:WP_101444364.1
          Length = 343

 Score =  416 bits (1069), Expect = e-121
 Identities = 204/338 (60%), Positives = 258/338 (76%), Gaps = 3/338 (0%)

Query: 1   MQQILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILGAPVKYHEGDC 60
           M++IL+TGGAGYIGSHT V LV AGYEPII+DNFSN+ +  L G+  ILG  V  H  DC
Sbjct: 1   MKKILVTGGAGYIGSHTVVELVEAGYEPIIIDNFSNTEERSLQGIAAILGREVTCHRIDC 60

Query: 61  NDRKFMQAVFE-ENDLQGVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKD 119
            D   ++ VFE E  + GVIHFAA KAVGES   PL YY NN+ SL+ LL+ M++F V  
Sbjct: 61  TDVAALRKVFEQETGIAGVIHFAAYKAVGESVAEPLKYYHNNVGSLVALLQVMEEFKVNK 120

Query: 120 IVFSSSCTVYGQPDKLPVKETTPRKDAESPYGNTKKICEDILTDHVKSGAPARVVALRYF 179
           +VFSSSCTVYG P +LPV E TP + A SPYGNTKKICE+ILTD   SG+    +ALRYF
Sbjct: 121 LVFSSSCTVYGIPAELPVTEQTPVQKANSPYGNTKKICEEILTDLATSGSDIHTIALRYF 180

Query: 180 NPIGAHPSSLIGELPLGVPANLIPFVTQTGAGIREKITVFGDDYNTPDGTCIRDYIHVMD 239
           NPIGAHPS+ IGELPLGVP NL+PF+TQT AGIRE++T+FG+DY+T DGTCIRDY+HV+D
Sbjct: 181 NPIGAHPSAKIGELPLGVPNNLVPFITQTAAGIREQLTIFGNDYDTQDGTCIRDYVHVVD 240

Query: 240 LADAHVKSI-QYLADQPENFIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGD 298
           LA AHV +I + L D+ EN I+ FNVGTG GNTV+E ++AFE+ + + LNY+IGPRR GD
Sbjct: 241 LAKAHVVAIDRLLTDKAEN-IEFFNVGTGTGNTVLEAVQAFERATGEKLNYKIGPRRPGD 299

Query: 299 IEKVWANTDKVSKVLGWTPQFGLEEALRDAWNWQLSLK 336
           + K++A+  K ++ LG+     LEEA++ AW+WQ+ L+
Sbjct: 300 VPKIYADVTKATEELGFKTTSTLEEAMKSAWDWQMHLQ 337


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: 377
Number of extensions: 7
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: 337
Length of database: 343
Length adjustment: 28
Effective length of query: 309
Effective length of database: 315
Effective search space:    97335
Effective search space used:    97335
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_101444364.1 BD749_RS10905 (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.3524480.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-126  407.1   0.0   2.5e-126  406.9   0.0    1.0  1  NCBI__GCF_002846395.1:WP_101444364.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101444364.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.9   0.0  2.5e-126  2.5e-126       1     330 [.       3     338 ..       3     340 .. 0.97

  Alignments for each domain:
  == domain 1  score: 406.9 bits;  conditional E-value: 2.5e-126
                             TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleee.k 70 
                                           kiLvtGgaGyiGsh+v++l e+g+e +++Dn s++++++l+ +  i   ev+  + d +d ++l++v+e+e  
  NCBI__GCF_002846395.1:WP_101444364.1   3 KILVTGGAGYIGSHTVVELVEAGYEPIIIDNFSNTEERSLQGIAAILgrEVTCHRIDCTDVAALRKVFEQEtG 75 
                                           79******************************************998899******************96516 PP

                             TIGR01179  71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespln.pi 142
                                           i  viHfaa++avgEsv+ePlkYY+nnv + + Ll++m++++v+kl+Fsss++vYg + ++p++E++p++ + 
  NCBI__GCF_002846395.1:WP_101444364.1  76 IAGVIHFAAYKAVGESVAEPLKYYHNNVGSLVALLQVMEEFKVNKLVFSSSCTVYGIPAELPVTEQTPVQkAN 148
                                           999*****************************************************************99899 PP

                             TIGR01179 143 npYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifG 214
                                           +pYG++k + E+il+dl+++ +++++++LRYFn++GA+++ +iGe + + + +l++ ++++a+g re+l+ifG
  NCBI__GCF_002846395.1:WP_101444364.1 149 SPYGNTKKICEEILTDLATSGSDIHTIALRYFNPIGAHPSAKIGELPLGVPnNLVPFITQTAAGIREQLTIFG 221
                                           9**************************************************9********************* PP

                             TIGR01179 215 tdyptkDGtcvRDyiHveDlaeaHlaalealeeg..gesevynlGagqgfsvkevieavkkvsgkdikvelad 285
                                           +dy+t+DGtc+RDy+Hv Dla+aH+ a++ l +   ++ e +n+G+g+g+ v+e ++a+++++g+++++++ +
  NCBI__GCF_002846395.1:WP_101444364.1 222 NDYDTQDGTCIRDYVHVVDLAKAHVVAIDRLLTDkaENIEFFNVGTGTGNTVLEAVQAFERATGEKLNYKIGP 294
                                           *****************************987652367789******************************** PP

                             TIGR01179 286 rRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklke 330
                                           rR+GD+++++ad  k+++elg+k++ + Lee +ksawdW+ +l++
  NCBI__GCF_002846395.1:WP_101444364.1 295 RRPGDVPKIYADVTKATEELGFKTTST-LEEAMKSAWDWQMHLQN 338
                                           *************************99.************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (343 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: 23.63
//
[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