Alignments for a candidate for galE in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Shewanella loihica PV-4

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate 5209832 Shew_2285 UDP-glucose 4-epimerase (RefSeq)

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



>FitnessBrowser__PV4:5209832
          Length = 351

 Score =  400 bits (1028), Expect = e-116
 Identities = 196/335 (58%), Positives = 243/335 (72%)

Query: 1   MAILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLL 60
           M+ILVTGGAGYIGSH CVELL++G+++VVLDNLS +  E+L RV++IT   LTF E D+ 
Sbjct: 16  MSILVTGGAGYIGSHACVELLSAGHQLVVLDNLSRAKFESLARVEQITAAKLTFVEGDIR 75

Query: 61  DREAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIV 120
           D   +D++F+   I+AV+HFAGLKAVGES  +PL+YY NN+ G+  L  AM ++GVK +V
Sbjct: 76  DERTLDALFSHYHIDAVMHFAGLKAVGESTRLPLEYYDNNVVGSMRLLSAMTRHGVKTLV 135

Query: 121 FSSSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPF 180
           FSSSATVYG     PI E  P  +TNPYGQTKL++EQ+  +   A  + SV LLRYFNP 
Sbjct: 136 FSSSATVYGANPPLPIMEAAPRSSTNPYGQTKLVVEQMCAEWANAKQDVSVILLRYFNPV 195

Query: 181 GAHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAE 240
           GAH SG IGEDP G PNNL+PY+ QVA+G    LSVFG+DY T DGTGVRDYIHV+DL +
Sbjct: 196 GAHESGLIGEDPKGEPNNLLPYITQVAMGHRPYLSVFGSDYATTDGTGVRDYIHVMDLVQ 255

Query: 241 GHVKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFA 300
           GH+ AL ++    G   +NLG+G GYSVLEMV+AFE+ SGK++    A RRPGDIA  +A
Sbjct: 256 GHLAALTRLHGVAGCHTFNLGSGQGYSVLEMVRAFEQASGKDIALHMAPRRPGDIAASYA 315

Query: 301 DPAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGY 335
            P KA REL W   R L +M  DSWRWQ  N  GY
Sbjct: 316 CPDKAARELDWRVARDLSQMMQDSWRWQCRNPRGY 350


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: 423
Number of extensions: 11
Number of successful extensions: 1
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: 351
Length adjustment: 29
Effective length of query: 310
Effective length of database: 322
Effective search space:    99820
Effective search space used:    99820
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 5209832 Shew_2285 (UDP-glucose 4-epimerase (RefSeq))
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.11009.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   8.5e-138  444.7   0.0   9.6e-138  444.5   0.0    1.0  1  lcl|FitnessBrowser__PV4:5209832  Shew_2285 UDP-glucose 4-epimeras


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209832  Shew_2285 UDP-glucose 4-epimerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.5   0.0  9.6e-138  9.6e-138       2     331 ..      18     349 ..      17     350 .. 0.99

  Alignments for each domain:
  == domain 1  score: 444.5 bits;  conditional E-value: 9.6e-138
                        TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeekidaviHf 77 
                                      iLvtGgaGyiGsh +++ll++g+++vvlDnls+++ e+l ++e+it  ++++vegd++d+++l+a++++ +idav+Hf
  lcl|FitnessBrowser__PV4:5209832  18 ILVTGGAGYIGSHACVELLSAGHQLVVLDNLSRAKFESLARVEQITaaKLTFVEGDIRDERTLDALFSHYHIDAVMHF 95 
                                      9********************************************9999***************************** PP

                        TIGR01179  78 aaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrsklmvEri 155
                                      a+l+avgEs++ Pl+YY+nnvv++++Ll+am+++gvk+l+Fsssa+vYg +  +pi E++p +++npYG++kl+vE++
  lcl|FitnessBrowser__PV4:5209832  96 AGLKAVGESTRLPLEYYDNNVVGSMRLLSAMTRHGVKTLVFSSSATVYGANPPLPIMEAAPRSSTNPYGQTKLVVEQM 173
                                      ****************************************************************************** PP

                        TIGR01179 156 lkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGtdyptkDGtcvRDyiHve 232
                                        + ++a+++ +v++LRYFn++GA+e+g iGe++k+++ +l++++++va+g+r+ l++fG dy t+DGt+vRDyiHv+
  lcl|FitnessBrowser__PV4:5209832 174 CAEWANAKQDVSVILLRYFNPVGAHESGLIGEDPKGEPnNLLPYITQVAMGHRPYLSVFGSDYATTDGTGVRDYIHVM 251
                                      **************************************9*************************************** PP

                        TIGR01179 233 DlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadaskikrelgwkpk 310
                                      Dl ++Hlaal  l+  ++ +++nlG+gqg+sv+e+++a++++sgkdi+ ++a+rR+GD+a+ +a+++k+ rel+w++ 
  lcl|FitnessBrowser__PV4:5209832 252 DLVQGHLAALTRLHGVAGCHTFNLGSGQGYSVLEMVRAFEQASGKDIALHMAPRRPGDIAASYACPDKAARELDWRVA 329
                                      ****************************************************************************** PP

                        TIGR01179 311 yddLeeiiksawdWekklkeg 331
                                      +d L ++++++w+W+ ++++g
  lcl|FitnessBrowser__PV4:5209832 330 RD-LSQMMQDSWRWQCRNPRG 349
                                      *9.************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (351 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: 00:00:00.01
# Mc/sec: 6.31
//
[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