Alignments for a candidate for galE in Teredinibacter turnerae T7901

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Teredinibacter turnerae T7901

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate WP_015820685.1 TERTU_RS13920 UDP-glucose 4-epimerase GalE

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



>NCBI__GCF_000023025.1:WP_015820685.1
          Length = 339

 Score =  479 bits (1233), Expect = e-140
 Identities = 229/338 (67%), Positives = 275/338 (81%), Gaps = 2/338 (0%)

Query: 1   MAILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLL 60
           M+ILVTGGAGYIG+HTC+ELL++GYE+VV+DNL NS  EALNRV+E++GK +TF + D+ 
Sbjct: 1   MSILVTGGAGYIGTHTCIELLSAGYEVVVVDNLCNSKREALNRVEEVSGKKVTFIQGDVT 60

Query: 61  DREAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIV 120
           D+  +  +F+E  I+AVIHFAGLKAVGES  IPL+YYH NL GT  LCE ME +GV +++
Sbjct: 61  DKAVLRDIFSEYSIDAVIHFAGLKAVGESTQIPLRYYHTNLGGTVALCEVMEAFGVSRLL 120

Query: 121 FSSSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRD-LHTADNEWSVALLRYFNP 179
           FSSSATVYG P ++PI E FP  ATNPYG++KLM+E+ILRD      N+W V LLRYFNP
Sbjct: 121 FSSSATVYGDPASAPILETFPTSATNPYGRSKLMVEEILRDACRVPGNDWRVGLLRYFNP 180

Query: 180 FGAHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLA 239
            GAHPSGR+GEDP GIPNNL+PYVAQVAVGKL +L VFG+DYPT DGTGVRDYIHVVDLA
Sbjct: 181 IGAHPSGRLGEDPQGIPNNLLPYVAQVAVGKLAKLRVFGDDYPTVDGTGVRDYIHVVDLA 240

Query: 240 EGHVKALEKVLNSTGAD-AYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATC 298
            GHV+ALEK+LN   A   YNLGTG GYSVL++V AF K  GKE+PY  A+RRPGDIA C
Sbjct: 241 RGHVRALEKLLNCQPACLTYNLGTGQGYSVLQIVDAFAKACGKEIPYEIAERRPGDIAEC 300

Query: 299 FADPAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGYK 336
           +ADPA A  ELGW+A+ GLE+M AD+WRWQSSN  GY+
Sbjct: 301 YADPALATNELGWKAEYGLEQMVADTWRWQSSNPQGYE 338


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: 479
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: 339
Length adjustment: 28
Effective length of query: 311
Effective length of database: 311
Effective search space:    96721
Effective search space used:    96721
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_015820685.1 TERTU_RS13920 (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.28361.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-141  457.4   0.0   1.3e-141  457.2   0.0    1.0  1  lcl|NCBI__GCF_000023025.1:WP_015820685.1  TERTU_RS13920 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023025.1:WP_015820685.1  TERTU_RS13920 UDP-glucose 4-epimerase GalE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.2   0.0  1.3e-141  1.3e-141       2     331 ..       3     336 ..       2     337 .. 0.98

  Alignments for each domain:
  == domain 1  score: 457.2 bits;  conditional E-value: 1.3e-141
                                 TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavlee 68 
                                               iLvtGgaGyiG h++ +ll++g+evvv+Dnl+++++eal+++e+++  +v++++gd++dk+ l+++++e
  lcl|NCBI__GCF_000023025.1:WP_015820685.1   3 ILVTGGAGYIGTHTCIELLSAGYEVVVVDNLCNSKREALNRVEEVSgkKVTFIQGDVTDKAVLRDIFSE 71 
                                               9*******************************************9999********************* PP

                                 TIGR01179  69 ekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEes 137
                                                +idaviHfa+l+avgEs++ Pl+YY+ n+ +t+ L+e+m+++gv +l+Fsssa+vYg++ + pi E++
  lcl|NCBI__GCF_000023025.1:WP_015820685.1  72 YSIDAVIHFAGLKAVGESTQIPLRYYHTNLGGTVALCEVMEAFGVSRLLFSSSATVYGDPASAPILETF 140
                                               ********************************************************************* PP

                                 TIGR01179 138 plnpinpYGrsklmvErilkdlkka.dkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevav 204
                                               p++++npYGrsklmvE+il+d+ ++  ++++v +LRYFn++GA+++g++Ge++++++ +l+++va+vav
  lcl|NCBI__GCF_000023025.1:WP_015820685.1 141 PTSATNPYGRSKLMVEEILRDACRVpGNDWRVGLLRYFNPIGAHPSGRLGEDPQGIPnNLLPYVAQVAV 209
                                               *********************9776379*****************************9*********** PP

                                 TIGR01179 205 gkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeg.gesevynlGagqgfsvkevieavk 272
                                               gk+ kl++fG+dypt DGt+vRDyiHv Dla +H++ale+l +      +ynlG+gqg+sv+++++a+ 
  lcl|NCBI__GCF_000023025.1:WP_015820685.1 210 GKLAKLRVFGDDYPTVDGTGVRDYIHVVDLARGHVRALEKLLNCqPACLTYNLGTGQGYSVLQIVDAFA 278
                                               *****************************************998356679******************* PP

                                 TIGR01179 273 kvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331
                                               k++gk+i++e+a+rR+GD+a+++ad++ +++elgwk++y+ Le++++++w+W++++++g
  lcl|NCBI__GCF_000023025.1:WP_015820685.1 279 KACGKEIPYEIAERRPGDIAECYADPALATNELGWKAEYG-LEQMVADTWRWQSSNPQG 336
                                               ****************************************.**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (339 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: 7.00
//
[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