Alignments for a candidate for galE in Thiothrix lacustris DSM 21227

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Thiothrix lacustris DSM 21227

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate WP_028488019.1 Q394_RS0103275 UDP-glucose 4-epimerase GalE

Query= metacyc::BSU38860-MONOMER
         (339 letters)



>NCBI__GCF_000621325.1:WP_028488019.1
          Length = 343

 Score =  446 bits (1147), Expect = e-130
 Identities = 218/336 (64%), Positives = 264/336 (78%), Gaps = 3/336 (0%)

Query: 3   ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGK-DLTFYEADLLD 61
           ILVTGGAGYIGSHTCVELL +G+++VVLDNL NSS E+L RV EI+G+  + FYE D+ D
Sbjct: 7   ILVTGGAGYIGSHTCVELLAAGFQVVVLDNLCNSSPESLRRVAEISGQASIPFYEGDIRD 66

Query: 62  REAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVF 121
              +D +F E  I +VIHFAGLKAVGESV  PL+YY NN+ GT  L +AM+++GV+ IVF
Sbjct: 67  PVLLDRIFKEQAIYSVIHFAGLKAVGESVEKPLEYYDNNVAGTVSLLQAMQRHGVRNIVF 126

Query: 122 SSSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPFG 181
           SSSATVYG P T+PI E FPL ATNPYG++KLM+E++L DL+ AD  W +ALLRYFNP G
Sbjct: 127 SSSATVYGDPHTTPIQEHFPLSATNPYGRSKLMIEEMLGDLYKADPAWKIALLRYFNPVG 186

Query: 182 AHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAEG 241
           AH SG+IGEDP G+PNNLMPY+A+VAVG+ E LSVFG DYPT+DGTGVRDYIHVVDLA+G
Sbjct: 187 AHESGKIGEDPQGVPNNLMPYIARVAVGQYEYLSVFGGDYPTQDGTGVRDYIHVVDLAKG 246

Query: 242 HVKALEKVLNSTGAD--AYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCF 299
           HVKALE  L     +    NLGTG GYSVL+MVKAF + SG+EVPYR   RR GDIA C+
Sbjct: 247 HVKALEAFLRGDVPNLLLINLGTGQGYSVLDMVKAFAEASGREVPYRIVARRAGDIACCY 306

Query: 300 ADPAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGY 335
           ADPA A++ + W+A++ L EMC D+W WQ  N  GY
Sbjct: 307 ADPALAEQLIHWKAEKNLVEMCQDTWHWQKHNPQGY 342


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: 464
Number of extensions: 11
Number of successful extensions: 3
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: 339
Length of database: 343
Length adjustment: 29
Effective length of query: 310
Effective length of database: 314
Effective search space:    97340
Effective search space used:    97340
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_028488019.1 Q394_RS0103275 (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.26318.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-142  459.7   0.0   2.6e-142  459.5   0.0    1.0  1  lcl|NCBI__GCF_000621325.1:WP_028488019.1  Q394_RS0103275 UDP-glucose 4-epi


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000621325.1:WP_028488019.1  Q394_RS0103275 UDP-glucose 4-epimerase GalE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.5   0.0  2.6e-142  2.6e-142       1     331 [.       6     341 ..       6     342 .. 0.98

  Alignments for each domain:
  == domain 1  score: 459.5 bits;  conditional E-value: 2.6e-142
                                 TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit...evklvegdladkekleavl 66 
                                               kiLvtGgaGyiGsh++++ll++g++vvvlDnl+++s e+l+++ +i+   ++ ++egd++d   l++++
  lcl|NCBI__GCF_000621325.1:WP_028488019.1   6 KILVTGGAGYIGSHTCVELLAAGFQVVVLDNLCNSSPESLRRVAEISgqaSIPFYEGDIRDPVLLDRIF 74 
                                               79*******************************************9998899***************** PP

                                 TIGR01179  67 eeekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisE 135
                                               +e++i +viHfa+l+avgEsv++Pl+YY+nnv +t++Ll+amq++gv++++Fsssa+vYg+++++pi+E
  lcl|NCBI__GCF_000621325.1:WP_028488019.1  75 KEQAIYSVIHFAGLKAVGESVEKPLEYYDNNVAGTVSLLQAMQRHGVRNIVFSSSATVYGDPHTTPIQE 143
                                               ********************************************************************* PP

                                 TIGR01179 136 esplnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaeva 203
                                               ++pl+++npYGrsklm+E++l dl kad+++k+++LRYFn++GA+e+g+iGe++++ + +l++++a+va
  lcl|NCBI__GCF_000621325.1:WP_028488019.1 144 HFPLSATNPYGRSKLMIEEMLGDLYKADPAWKIALLRYFNPVGAHESGKIGEDPQGVPnNLMPYIARVA 212
                                               **********************************************************9********** PP

                                 TIGR01179 204 vgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeg..gesevynlGagqgfsvkeviea 270
                                               vg+ e l++fG+dypt+DGt+vRDyiHv Dla++H++alea  +g   +  + nlG+gqg+sv+++++a
  lcl|NCBI__GCF_000621325.1:WP_028488019.1 213 VGQYEYLSVFGGDYPTQDGTGVRDYIHVVDLAKGHVKALEAFLRGdvPNLLLINLGTGQGYSVLDMVKA 281
                                               ******************************************99833456678**************** PP

                                 TIGR01179 271 vkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331
                                               + ++sg+++++++ +rRaGD+a+++ad++ +++ + wk++ + L e+++++w+W+k++++g
  lcl|NCBI__GCF_000621325.1:WP_028488019.1 282 FAEASGREVPYRIVARRAGDIACCYADPALAEQLIHWKAEKN-LVEMCQDTWHWQKHNPQG 341
                                               ****************************************99.***************987 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.04
//
[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