Alignments for a candidate for deoB in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Escherichia coli BW25113

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 18404 b4383 phosphopentomutase (NCBI)

Query= BRENDA::P0A6K6
         (407 letters)



>FitnessBrowser__Keio:18404
          Length = 407

 Score =  839 bits (2168), Expect = 0.0
 Identities = 407/407 (100%), Positives = 407/407 (100%)

Query: 1   MKRAFIMVLDSFGIGATEDAERFGDVGADTLGHIAEACAKGEADNGRKGPLNLPNLTRLG 60
           MKRAFIMVLDSFGIGATEDAERFGDVGADTLGHIAEACAKGEADNGRKGPLNLPNLTRLG
Sbjct: 1   MKRAFIMVLDSFGIGATEDAERFGDVGADTLGHIAEACAKGEADNGRKGPLNLPNLTRLG 60

Query: 61  LAKAHEGSTGFIPAGMDGNAEVIGAYAWAHEMSSGKDTPSGHWEIAGVPVLFEWGYFSDH 120
           LAKAHEGSTGFIPAGMDGNAEVIGAYAWAHEMSSGKDTPSGHWEIAGVPVLFEWGYFSDH
Sbjct: 61  LAKAHEGSTGFIPAGMDGNAEVIGAYAWAHEMSSGKDTPSGHWEIAGVPVLFEWGYFSDH 120

Query: 121 ENSFPQELLDKLVERANLPGYLGNCHSSGTVILDQLGEEHMKTGKPIFYTSADSVFQIAC 180
           ENSFPQELLDKLVERANLPGYLGNCHSSGTVILDQLGEEHMKTGKPIFYTSADSVFQIAC
Sbjct: 121 ENSFPQELLDKLVERANLPGYLGNCHSSGTVILDQLGEEHMKTGKPIFYTSADSVFQIAC 180

Query: 181 HEETFGLDKLYELCEIAREELTNGGYNIGRVIARPFIGDKAGNFQRTGNRHDLAVEPPAP 240
           HEETFGLDKLYELCEIAREELTNGGYNIGRVIARPFIGDKAGNFQRTGNRHDLAVEPPAP
Sbjct: 181 HEETFGLDKLYELCEIAREELTNGGYNIGRVIARPFIGDKAGNFQRTGNRHDLAVEPPAP 240

Query: 241 TVLQKLVDEKHGQVVSVGKIADIYANCGITKKVKATGLDALFDATIKEMKEAGDNTIVFT 300
           TVLQKLVDEKHGQVVSVGKIADIYANCGITKKVKATGLDALFDATIKEMKEAGDNTIVFT
Sbjct: 241 TVLQKLVDEKHGQVVSVGKIADIYANCGITKKVKATGLDALFDATIKEMKEAGDNTIVFT 300

Query: 301 NFVDFDSSWGHRRDVAGYAAGLELFDRRLPELMSLLRDDDILILTADHGCDPTWTGTDHT 360
           NFVDFDSSWGHRRDVAGYAAGLELFDRRLPELMSLLRDDDILILTADHGCDPTWTGTDHT
Sbjct: 301 NFVDFDSSWGHRRDVAGYAAGLELFDRRLPELMSLLRDDDILILTADHGCDPTWTGTDHT 360

Query: 361 REHIPVLVYGPKVKPGSLGHRETFADIGQTLAKYFGTSDMEYGKAMF 407
           REHIPVLVYGPKVKPGSLGHRETFADIGQTLAKYFGTSDMEYGKAMF
Sbjct: 361 REHIPVLVYGPKVKPGSLGHRETFADIGQTLAKYFGTSDMEYGKAMF 407


Lambda     K      H
   0.318    0.138    0.422 

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: 847
Number of extensions: 31
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: 407
Length of database: 407
Length adjustment: 31
Effective length of query: 376
Effective length of database: 376
Effective search space:   141376
Effective search space used:   141376
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 18404 b4383 (phosphopentomutase (NCBI))
to HMM TIGR01696 (deoB: phosphopentomutase (EC 5.4.2.7))

# 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/TIGR01696.hmm
# target sequence database:        /tmp/gapView.29556.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01696  [M=381]
Accession:   TIGR01696
Description: deoB: phosphopentomutase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     3e-214  696.9   0.0   3.4e-214  696.7   0.0    1.0  1  lcl|FitnessBrowser__Keio:18404  b4383 phosphopentomutase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:18404  b4383 phosphopentomutase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  696.7   0.0  3.4e-214  3.4e-214       1     381 []       3     405 ..       3     405 .. 1.00

  Alignments for each domain:
  == domain 1  score: 696.7 bits;  conditional E-value: 3.4e-214
                       TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk..........lnlpnleklGlgkiee......lagvdavee 63 
                                     r+f++vlds+GiG++eda++f+d+Gadtlghiaea++k          lnlpnl++lGl+k++e      +ag+d+++e
  lcl|FitnessBrowser__Keio:18404   3 RAFIMVLDSFGIGATEDAERFGDVGADTLGHIAEACAKgeadngrkgpLNLPNLTRLGLAKAHEgstgfiPAGMDGNAE 81 
                                     89*******************************************************************99******** PP

                       TIGR01696  64 vlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkpasGtvildelGeeh 138
                                     v+++ya+++e+ssGkdt++GhweiaG+++l+e+++fs   n+fp+elldkl+era+++ +lgn+++sGtvild+lGeeh
  lcl|FitnessBrowser__Keio:18404  82 VIGAYAWAHEMSSGKDTPSGHWEIAGVPVLFEWGYFSdheNSFPQELLDKLVERANLPgYLGNCHSSGTVILDQLGEEH 160
                                     *************************************9999************************************** PP

                       TIGR01696 139 mktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfkrtsnrhdyalkpfa 216
                                     mktGk+i+ytsadsv+qia+hee+++l++lyelce+are+l++++y+iGr+iarpf+G+ aGnf+rt+nrhd+a++p+a
  lcl|FitnessBrowser__Keio:18404 161 MKTGKPIFYTSADSVFQIACHEETFGLDKLYELCEIAREELTNGGYNIGRVIARPFIGDkAGNFQRTGNRHDLAVEPPA 239
                                     ******************************************************************************* PP

                       TIGR01696 217 ktvldklkdeky.dvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftg.isfanlvdfdalyGhrrdkeGy 293
                                     +tvl+kl+dek+ +v+s+Gkiadiy+++Gitkkv+++++++++d++ike+ke++++ i+f+n+vdfd+++Ghrrd++Gy
  lcl|FitnessBrowser__Keio:18404 240 PTVLQKLVDEKHgQVVSVGKIADIYANCGITKKVKATGLDALFDATIKEMKEAGDNtIVFTNFVDFDSSWGHRRDVAGY 318
                                     ******************************************************************************* PP

                       TIGR01696 294 aaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkvkkgqalesaetfadiGatladnfn 372
                                     aa+le fd+rlpel+s+lr+dd+liltadhG+dpt+tGtdhtre+ipvlvy+pkvk+g +l+++etfadiG+tla++f+
  lcl|FitnessBrowser__Keio:18404 319 AAGLELFDRRLPELMSLLRDDDILILTADHGCDPTWTGTDHTREHIPVLVYGPKVKPG-SLGHRETFADIGQTLAKYFG 396
                                     **********************************************************.******************** PP

                       TIGR01696 373 tskpeyGks 381
                                     ts++eyGk+
  lcl|FitnessBrowser__Keio:18404 397 TSDMEYGKA 405
                                     *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (407 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: 11.33
//
[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