Alignments for a candidate for galE in Synechococcus elongatus PCC 7942

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Synechococcus elongatus PCC 7942

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate Synpcc7942_0320 Synpcc7942_0320 UDP-galactose 4-epimerase

Query= curated2:Q59745
         (327 letters)



>FitnessBrowser__SynE:Synpcc7942_0320
          Length = 332

 Score =  369 bits (946), Expect = e-107
 Identities = 184/330 (55%), Positives = 228/330 (69%), Gaps = 4/330 (1%)

Query: 1   MAGETVLVVGGAGYIGSHTCLDLANKGYRPVVFDNFSNGHREF---VRWGPAEEGDIRDR 57
           +AG T+LV GGAGYIGSHT   L  +GY+P+V DN SNG R     V   P   GD RDR
Sbjct: 1   VAGATILVTGGAGYIGSHTVRALQAQGYQPIVLDNLSNGQRAIAAEVLQVPLIVGDTRDR 60

Query: 58  ARLDEVLAKHKPAAILHFAALIEVGESVKDPVSFYENNVIGTLTLLSAAQAAGINAFVFS 117
             LD + A+H   A++HFAA IEVGESV+DP +FY NNV G+LTLL A  AAG    VFS
Sbjct: 61  LLLDRLFAEHPIQAVIHFAASIEVGESVRDPGNFYANNVSGSLTLLQAMVAAGCQQLVFS 120

Query: 118 STCATYGLPQSVPLDETHRQVPINPYGRTKYIVEQALADYDQYGSLRSVVLRYFNAAGAD 177
           STCATYGLPQ +P+ E H Q PINPYGR+K++VEQ L D+     LRSV+ RYFNAAGAD
Sbjct: 121 STCATYGLPQVIPIPEDHPQAPINPYGRSKWMVEQFLQDFQAAYGLRSVIFRYFNAAGAD 180

Query: 178 FEGRIGEWHQPETHAIPLAIDAALGRRQGFKVFGSDYETRDGTCVRDYIHVLDLADAHVR 237
            +G +GE H PETH IPL + AA G+R   +V+G+DY T DGTC+RDYIHV DLADAHVR
Sbjct: 181 PKGDLGEAHDPETHLIPLVLQAAAGQRPSIQVYGTDYPTSDGTCIRDYIHVCDLADAHVR 240

Query: 238 AVEYLLKGGDSVALNLGTGTGTTVKELLGAIEEVSNRPFPVEYIGRREGDSHTLVANNDK 297
            + YL  GG + A NLG G G +VKE++   E V+ R  PV+   RR GD+  LV ++DK
Sbjct: 241 GLTYLADGGATTAFNLGNGNGFSVKEVIATAERVTQRSIPVQLSDRRPGDAIALVGSSDK 300

Query: 298 ARDVLGWVPQY-DLSEIIRSAWDWHAKSNQ 326
           AR +LGW PQ+  L  +I+ AW W  + ++
Sbjct: 301 ARQILGWEPQFPSLETMIQHAWQWQQRCDR 330


Lambda     K      H
   0.319    0.137    0.415 

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: 367
Number of extensions: 19
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: 327
Length of database: 332
Length adjustment: 28
Effective length of query: 299
Effective length of database: 304
Effective search space:    90896
Effective search space used:    90896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate Synpcc7942_0320 Synpcc7942_0320 (UDP-galactose 4-epimerase)
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.20869.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-140  453.3   0.0   2.2e-140  453.2   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_0320  Synpcc7942_0320 UDP-galactose 4-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_0320  Synpcc7942_0320 UDP-galactose 4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.2   0.0  2.2e-140  2.2e-140       2     329 ..       6     329 ..       5     332 .] 0.98

  Alignments for each domain:
  == domain 1  score: 453.2 bits;  conditional E-value: 2.2e-140
                                 TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeek 70 
                                               iLvtGgaGyiGsh+vr+l+++g++ +vlDnls+g++ +  ++    +v l+ gd +d+  l+++++e+ 
  lcl|FitnessBrowser__SynE:Synpcc7942_0320   6 ILVTGGAGYIGSHTVRALQAQGYQPIVLDNLSNGQRAIAAEVL---QVPLIVGDTRDRLLLDRLFAEHP 71 
                                               9*********************************998776665...7********************** PP

                                 TIGR01179  71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139
                                               i+aviHfaa+i+vgEsv++P ++Y+nnv+++l+Ll+am++ag+++l+Fss++a+Yg ++ +pi E++p+
  lcl|FitnessBrowser__SynE:Synpcc7942_0320  72 IQAVIHFAASIEVGESVRDPGNFYANNVSGSLTLLQAMVAAGCQQLVFSSTCATYGLPQVIPIPEDHPQ 140
                                               ********************************************************************* PP

                                 TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkre 208
                                               +pinpYGrsk mvE+ l+d++ a ++l+ vi RYFn+aGAd++g++Gea+ ++thli+lv+++a+g+r+
  lcl|FitnessBrowser__SynE:Synpcc7942_0320 141 APINPYGRSKWMVEQFLQDFQAA-YGLRSVIFRYFNAAGADPKGDLGEAHDPETHLIPLVLQAAAGQRP 208
                                               ********************999.********************************************* PP

                                 TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgk 277
                                               +++++Gtdypt+DGtc+RDyiHv+Dla+aH++ l +l++gg ++++nlG+g+gfsvkevi ++++v+ +
  lcl|FitnessBrowser__SynE:Synpcc7942_0320 209 SIQVYGTDYPTSDGTCIRDYIHVCDLADAHVRGLTYLADGGATTAFNLGNGNGFSVKEVIATAERVTQR 277
                                               ********************************************************************* PP

                                 TIGR01179 278 dikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklk 329
                                               +i+v+l+drR+GD  +lv++++k+++ lgw+p++  Le++i+ aw+W++++ 
  lcl|FitnessBrowser__SynE:Synpcc7942_0320 278 SIPVQLSDRRPGDAIALVGSSDKARQILGWEPQFPSLETMIQHAWQWQQRCD 329
                                               *************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (332 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.78
//
[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