Alignments for a candidate for galE in Sulfurihydrogenibium azorense Az-Fu1

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Sulfurihydrogenibium azorense Az-Fu1

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_012673695.1 SULAZ_RS04435 UDP-glucose 4-epimerase GalE

Query= SwissProt::Q7WTB1
         (330 letters)



>NCBI__GCF_000021545.1:WP_012673695.1
          Length = 341

 Score =  273 bits (697), Expect = 6e-78
 Identities = 144/335 (42%), Positives = 205/335 (61%), Gaps = 15/335 (4%)

Query: 1   MKVLVIGGAGYIGSHAVRELVKEGN-DVLVLDALYTGHRKAV------------DPKAKF 47
           M +L+ GGAGYIGSH V++L+ E N ++ ++D L TG  K +            +    F
Sbjct: 1   MNILITGGAGYIGSHVVKQLLDETNHNITIIDNLSTGSIKTIKTLKEIAKINNKEENLDF 60

Query: 48  YQGDIEDTFLVSKILRDEKIDAVMHFAAYSLVPESVKKPLKYYDNNVTGMISLLQAMNDA 107
            + D+ +  L+  I++ +K DAV+HFAA  +VPESVK P+KYY NN     +L++   D 
Sbjct: 61  IEADLSNFPLIEGIIKAKKFDAVIHFAASIIVPESVKNPIKYYMNNTVNTTNLIKLCLDN 120

Query: 108 NVKYLVFSSSAATYGIPKKLPITEDTPLNPINPYGETKMMMEKIMAWADKA-DGIKYTAL 166
           NV   +FSS+AA YG P ++P+ E TP  PINPYG +K+M E ++     A    KY  L
Sbjct: 121 NVNKFIFSSTAAVYGQPYEIPVKETTPTKPINPYGMSKLMSETVLKDCGLAYPDFKYIIL 180

Query: 167 RYFNVAGASSDGSIGEDHAPETHLIPNILKSAISGDGKFTIFGDDYDTKDGTNVRDYVQV 226
           RYFNVAGA     IG+     THLI    ++A+    K  +FG DY TKDGT +RDY+ V
Sbjct: 181 RYFNVAGADIKIRIGQRFPNATHLIKVAAETAVGKREKMYVFGTDYPTKDGTCIRDYIHV 240

Query: 227 EDLIDAHILALKHMMKTNKSDVFNLGTAHGYSNLEILESAKKVTGIDIPYTMGPRRGGDP 286
           +DL DAHI AL++ +  N SDVFN G  +GYS LE++ + KKV+G+D       RR GDP
Sbjct: 241 DDLADAHIKALEY-LTDNDSDVFNCGYGYGYSVLEVINTMKKVSGVDFKVEFTGRREGDP 299

Query: 287 DSLVADSTKARTVLGWKPKHENVDDVIATAWKWHK 321
             L+AD++K +  + W+PK+ N++ +  TA +W K
Sbjct: 300 AILIADNSKIKNKMKWQPKYNNLELICKTALEWEK 334


Lambda     K      H
   0.315    0.134    0.395 

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: 342
Number of extensions: 12
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: 330
Length of database: 341
Length adjustment: 28
Effective length of query: 302
Effective length of database: 313
Effective search space:    94526
Effective search space used:    94526
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_012673695.1 SULAZ_RS04435 (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.29964.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-148  479.8   0.2   1.9e-148  479.6   0.2    1.0  1  lcl|NCBI__GCF_000021545.1:WP_012673695.1  SULAZ_RS04435 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021545.1:WP_012673695.1  SULAZ_RS04435 UDP-glucose 4-epimerase GalE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.6   0.2  1.9e-148  1.9e-148       1     329 [.       2     337 ..       2     340 .. 0.97

  Alignments for each domain:
  == domain 1  score: 479.6 bits;  conditional E-value: 1.9e-148
                                 TIGR01179   1 kiLvtGgaGyiGshvvrqllek.gkevvvlDnlskgskealkalekit.......evklvegdladkek 61 
                                               +iL+tGgaGyiGshvv+qll++ ++++ ++Dnls+gs +++k+l++i        ++ ++e+dl++   
  lcl|NCBI__GCF_000021545.1:WP_012673695.1   2 NILITGGAGYIGSHVVKQLLDEtNHNITIIDNLSTGSIKTIKTLKEIAkinnkeeNLDFIEADLSNFPL 70 
                                               59****************98661577****************9999877777777899*********** PP

                                 TIGR01179  62 leavleeekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesek 130
                                               +e +++++k+daviHfaa+i v+Esvk+P+kYY+nn+vnt++L++++ + +v+k+iFss+aavYg++ +
  lcl|NCBI__GCF_000021545.1:WP_012673695.1  71 IEGIIKAKKFDAVIHFAASIIVPESVKNPIKYYMNNTVNTTNLIKLCLDNNVNKFIFSSTAAVYGQPYE 139
                                               ********************************************************************* PP

                                 TIGR01179 131 vpisEesplnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklv 199
                                               +p++E++p++pinpYG sklm+E +lkd+  a +++k++iLRYFnvaGAd + +iG++ +nathlik++
  lcl|NCBI__GCF_000021545.1:WP_012673695.1 140 IPVKETTPTKPINPYGMSKLMSETVLKDCGLAYPDFKYIILRYFNVAGADIKIRIGQRFPNATHLIKVA 208
                                               ********************************************************************* PP

                                 TIGR01179 200 aevavgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevi 268
                                               ae+avgkrek+ +fGtdyptkDGtc+RDyiHv+Dla+aH++ale+l++ ++s+v+n+G+g g+sv+evi
  lcl|NCBI__GCF_000021545.1:WP_012673695.1 209 AETAVGKREKMYVFGTDYPTKDGTCIRDYIHVDDLADAHIKALEYLTD-NDSDVFNCGYGYGYSVLEVI 276
                                               **********************************************96.9******************* PP

                                 TIGR01179 269 eavkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklk 329
                                               +++kkvsg+d+kve++ rR+GDpa l+ad+skik+++ w+pky++Le i+k+a++Wekkl 
  lcl|NCBI__GCF_000021545.1:WP_012673695.1 277 NTMKKVSGVDFKVEFTGRREGDPAILIADNSKIKNKMKWQPKYNNLELICKTALEWEKKLL 337
                                               *********************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (341 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: 7.69
//
[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 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