Alignments for a candidate for galE in Maridesulfovibrio zosterae DSM 11974

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Maridesulfovibrio zosterae DSM 11974

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_027722814.1 H589_RS0115165 UDP-glucose 4-epimerase GalE

Query= curated2:O84903
         (331 letters)



>NCBI__GCF_000425265.1:WP_027722814.1
          Length = 330

 Score =  304 bits (778), Expect = 2e-87
 Identities = 149/321 (46%), Positives = 207/321 (64%), Gaps = 1/321 (0%)

Query: 1   MTIAVLGGAGYIGSHTVKQLLAAGEDVVVLDNLITGHRKAVDPRARFYQGDIRDYHFLSQ 60
           +++ V GGAGYIGSH  + +  +G DV V DNL TGH +A+    +F +GD+R+ + +++
Sbjct: 7   LSLLVCGGAGYIGSHMARMIAESGHDVTVFDNLSTGHMEALK-WGKFIKGDLRNPNDVAK 65

Query: 61  VFSQEKIDGIVHFAAFSIVPESMKDPLKYFDNNTGGMITLLEAMNQFGIKKIVFSSTAAT 120
            F     D + HF+   +V ES++ P +Y+DNN  G I LLEAM   G+ K VFSSTAA 
Sbjct: 66  AFEDSNYDAVFHFSGLIVVSESVEKPFEYYDNNVTGTINLLEAMRANGVNKFVFSSTAAV 125

Query: 121 YGEPKQVPIKETDPQVPTNPYGESKLAMEKIMHWADVAYGLKFVALRYFNVAGAMPDGSI 180
           YG+P    I E  P  P NPYG+SKL +E+I+    VAYGL  V  RYFN AGA PD  I
Sbjct: 126 YGDPVMDMITEDHPLKPLNPYGKSKLFVEEILQDYAVAYGLDSVCFRYFNAAGAHPDSLI 185

Query: 181 GEDHHPETHIVPIILQVAAGTRTGLQIYGDDYPTKDGTNVRDYVHVVDLADAHILALKYL 240
           GE H PETH++P IL         L+I+G+DYPT DGT VRDY+H++DL DAH+ A+ Y+
Sbjct: 186 GEAHKPETHLIPNILLSGIDDGRKLKIFGNDYPTPDGTCVRDYIHILDLCDAHLSAISYM 245

Query: 241 DAGNKSSAFNIGSAHGFSNLEILNAARKVTGQEIPATMGPRRAGDPSTLIASSEKARDIL 300
           +    +  FN+G+  GFS LE++ A+ +V G +I     P RAGD   L+A S KA   L
Sbjct: 246 ENKEGAHVFNLGNGQGFSILEVIKASSEVMGNKIEFDYEPARAGDSPRLVADSSKAVREL 305

Query: 301 GWKPNYDDIDKIIETAWNWHE 321
            W+P ++D+ ++IETA+ WH+
Sbjct: 306 KWQPKFNDLREMIETAYRWHK 326


Lambda     K      H
   0.318    0.136    0.409 

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: 363
Number of extensions: 17
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: 331
Length of database: 330
Length adjustment: 28
Effective length of query: 303
Effective length of database: 302
Effective search space:    91506
Effective search space used:    91506
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 WP_027722814.1 H589_RS0115165 (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.1445631.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.8e-135  435.9   0.0   4.6e-135  435.6   0.0    1.0  1  NCBI__GCF_000425265.1:WP_027722814.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000425265.1:WP_027722814.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.6   0.0  4.6e-135  4.6e-135       2     327 ..       9     327 ..       8     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 435.6 bits;  conditional E-value: 4.6e-135
                             TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidav 74 
                                           +Lv GgaGyiGsh++r + e+g++v v+Dnls+g+ ealk+++      +++gdl++ + +++++e+++ dav
  NCBI__GCF_000425265.1:WP_027722814.1   9 LLVCGGAGYIGSHMARMIAESGHDVTVFDNLSTGHMEALKWGK------FIKGDLRNPNDVAKAFEDSNYDAV 75 
                                           89*****************************************......************************ PP

                             TIGR01179  75 iHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGr 147
                                            Hf++li v Esv++P +YY+nnv++t++Lleam++ gv+k++Fss+aavYg++    i+E++pl+p npYG+
  NCBI__GCF_000425265.1:WP_027722814.1  76 FHFSGLIVVSESVEKPFEYYDNNVTGTINLLEAMRANGVNKFVFSSTAAVYGDPVMDMITEDHPLKPLNPYGK 148
                                           ************************************************************************* PP

                             TIGR01179 148 sklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptk 220
                                           skl vE+il+d++ a ++l+ v  RYFn+aGA+++  iGea+k++thli+ ++   +    kl+ifG+dypt+
  NCBI__GCF_000425265.1:WP_027722814.1 149 SKLFVEEILQDYAVA-YGLDSVCFRYFNAAGAHPDSLIGEAHKPETHLIPNILLSGIDDGRKLKIFGNDYPTP 220
                                           ************999.********************************************************* PP

                             TIGR01179 221 DGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpas 293
                                           DGtcvRDyiH+ Dl +aHl a+ ++e++++++v+nlG+gqgfs++evi+a ++v g++i++  ++ RaGD ++
  NCBI__GCF_000425265.1:WP_027722814.1 221 DGTCVRDYIHILDLCDAHLSAISYMENKEGAHVFNLGNGQGFSILEVIKASSEVMGNKIEFDYEPARAGDSPR 293
                                           ************************************************************************* PP

                             TIGR01179 294 lvadaskikrelgwkpkyddLeeiiksawdWekk 327
                                           lvad+sk+ rel w+pk++dL+e+i++a++W+kk
  NCBI__GCF_000425265.1:WP_027722814.1 294 LVADSSKAVRELKWQPKFNDLREMIETAYRWHKK 327
                                           ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (330 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: 18.90
//
[ok]

This GapMind analysis is from Apr 09 2024. 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