Alignments for a candidate for deoB in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Shewanella oneidensis MR-1

Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 200397 SO1219 phosphopentomutase (NCBI ptt file)

Query= reanno::MR1:200397
         (404 letters)



>FitnessBrowser__MR1:200397
          Length = 404

 Score =  823 bits (2125), Expect = 0.0
 Identities = 404/404 (100%), Positives = 404/404 (100%)

Query: 1   MKRTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEGKADTGRKGPLALPNLARLG 60
           MKRTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEGKADTGRKGPLALPNLARLG
Sbjct: 1   MKRTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEGKADTGRKGPLALPNLARLG 60

Query: 61  LAHAAMESTGAFAPGFADNVDLIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH 120
           LAHAAMESTGAFAPGFADNVDLIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH
Sbjct: 61  LAHAAMESTGAFAPGFADNVDLIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH 120

Query: 121 QNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQIAC 180
           QNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQIAC
Sbjct: 121 QNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQIAC 180

Query: 181 HEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAKTV 240
           HEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAKTV
Sbjct: 181 HEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAKTV 240

Query: 241 LDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTNFV 300
           LDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTNFV
Sbjct: 241 LDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTNFV 300

Query: 301 DFDSHYGHRRDVAGYAKGLEYFDARLPEMLALLDEDDLLILTADHGCDPTWQGTDHTREY 360
           DFDSHYGHRRDVAGYAKGLEYFDARLPEMLALLDEDDLLILTADHGCDPTWQGTDHTREY
Sbjct: 301 DFDSHYGHRRDVAGYAKGLEYFDARLPEMLALLDEDDLLILTADHGCDPTWQGTDHTREY 360

Query: 361 VPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI 404
           VPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI
Sbjct: 361 VPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI 404


Lambda     K      H
   0.318    0.137    0.412 

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: 810
Number of extensions: 23
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: 404
Length of database: 404
Length adjustment: 31
Effective length of query: 373
Effective length of database: 373
Effective search space:   139129
Effective search space used:   139129
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 200397 SO1219 (phosphopentomutase (NCBI ptt file))
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.71025.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                   -----------
   1.2e-171  556.7   0.0   1.3e-171  556.5   0.0    1.0  1  FitnessBrowser__MR1:200397  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__MR1:200397  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  556.5   0.0  1.3e-171  1.3e-171       1     381 []       3     402 ..       3     402 .. 0.98

  Alignments for each domain:
  == domain 1  score: 556.5 bits;  conditional E-value: 1.3e-171
                   TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk..........lnlpnleklGlgkiee......lagvdaveevlay 67 
                                 r+ +++lds+G+G+a daa+f+d+G+dt+ghia+a+++          l lpnl++lGl+++         +g  ++ + +++
  FitnessBrowser__MR1:200397   3 RTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEgkadtgrkgpLALPNLARLGLAHAAMestgafAPGFADNVDLIGA 85 
                                 6789*********************************99*********************9877689999999********** PP

                   TIGR01696  68 yaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkpasGtvildelGeehmktGkliv 146
                                 y++++e+ssGkdt++Ghwe+aG+++l+e+++fs   n+fp+el dk+  rag+  +lgn++asGt+il+elGeehm++Gk+i+
  FitnessBrowser__MR1:200397  86 YGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSehqNSFPKELTDKILARAGLDgFLGNCHASGTTILEELGEEHMRSGKPIF 168
                                 *********************************9999*****************9**************************** PP

                   TIGR01696 147 ytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfkrtsnrhdyalkpfaktvldklkdeky 228
                                 ytsadsv+qia+he +++le+ly+lce+are+l    y+iGr+iarpf G  + +f rt+nr+dy+l+p+aktvldklk ++ 
  FitnessBrowser__MR1:200397 169 YTSADSVFQIACHEGTFGLENLYRLCEIAREELE--PYNIGRVIARPFDGTgPSDFARTGNRKDYSLEPPAKTVLDKLKAAGG 249
                                 ********************************96..5*************99******************************* PP

                   TIGR01696 229 dvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftg.isfanlvdfdalyGhrrdkeGyaaaleefdarlpellsk 310
                                 +v+s+Gkiadiy+ +Gitkkv+++++++++d+++ e+k ++++ i+f+n+vdfd+ yGhrrd++Gya++le fdarlpe+l++
  FitnessBrowser__MR1:200397 250 EVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENtIVFTNFVDFDSHYGHRRDVAGYAKGLEYFDARLPEMLAL 332
                                 ******************************************99*************************************** PP

                   TIGR01696 311 lreddlliltadhGndptatGtdhtreyipvlvyspkvkkgqalesaetfadiGatladnfntskpeyGks 381
                                 l eddlliltadhG+dpt++Gtdhtrey+pvl+y+   k g +l+++++fadiG+++a +f+ + +eyG s
  FitnessBrowser__MR1:200397 333 LDEDDLLILTADHGCDPTWQGTDHTREYVPVLAYGAGLKAG-SLGRRNSFADIGQSIASYFKLEPMEYGES 402
                                 *****************************************.***************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (404 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.73
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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