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

GapMind for catabolism of small carbon sources

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

Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 5210370 Shew_2813 phosphopentomutase (RefSeq)

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



>FitnessBrowser__PV4:5210370
          Length = 405

 Score =  714 bits (1844), Expect = 0.0
 Identities = 348/404 (86%), Positives = 373/404 (92%)

Query: 1   MKRTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEGKADTGRKGPLALPNLARLG 60
           MKRTVIMMLDSFGVGAA DA  FGD GS+TFGHIAKACAEGKA+ GR+GPL LPNLA+LG
Sbjct: 1   MKRTVIMMLDSFGVGAAKDAEAFGDTGSNTFGHIAKACAEGKANDGREGPLKLPNLAKLG 60

Query: 61  LAHAAMESTGAFAPGFADNVDLIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH 120
           LA AA ESTG+FA GF D+V++IGAYGHA ELSSGKDTPSGHWEMAGVPVL+EWGYFS+ 
Sbjct: 61  LALAAKESTGSFAEGFGDDVEVIGAYGHADELSSGKDTPSGHWEMAGVPVLYEWGYFSDL 120

Query: 121 QNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQIAC 180
           ++SFPKELTDKIL RAGL GFLGNCHASGT ILEELGEEHM SG PIFYTSADSVFQIAC
Sbjct: 121 KDSFPKELTDKILERAGLSGFLGNCHASGTAILEELGEEHMTSGLPIFYTSADSVFQIAC 180

Query: 181 HEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAKTV 240
           HE TFGLENLY LC+IAREELEPYNIGRVIARPF GTGPSDFARTGNRKDY++EPP+KTV
Sbjct: 181 HEETFGLENLYTLCQIAREELEPYNIGRVIARPFVGTGPSDFARTGNRKDYAVEPPSKTV 240

Query: 241 LDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTNFV 300
           LDKLK AGGEVVSVGKIADIYA+CGITKKVKA GLEALFDATL +VK AG+ TIVFTNFV
Sbjct: 241 LDKLKEAGGEVVSVGKIADIYAHCGITKKVKATGLEALFDATLEQVKQAGDRTIVFTNFV 300

Query: 301 DFDSHYGHRRDVAGYAKGLEYFDARLPEMLALLDEDDLLILTADHGCDPTWQGTDHTREY 360
           DFDSHYGHRRD+AGYA+ LEYFD+RLPEMLALL E+DLL+LTADHGCDPTWQGTDHTRE 
Sbjct: 301 DFDSHYGHRRDIAGYARALEYFDSRLPEMLALLGEEDLLLLTADHGCDPTWQGTDHTRER 360

Query: 361 VPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI 404
           VPVLAYGAGL  GSLGRRNSFADIGQSIASYF LEPMEYGESF+
Sbjct: 361 VPVLAYGAGLAPGSLGRRNSFADIGQSIASYFGLEPMEYGESFV 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: 734
Number of extensions: 15
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: 405
Length adjustment: 31
Effective length of query: 373
Effective length of database: 374
Effective search space:   139502
Effective search space used:   139502
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 5210370 Shew_2813 (phosphopentomutase (RefSeq))
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.16044.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-169  550.1   0.0   1.3e-169  550.0   0.0    1.0  1  lcl|FitnessBrowser__PV4:5210370  Shew_2813 phosphopentomutase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210370  Shew_2813 phosphopentomutase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  550.0   0.0  1.3e-169  1.3e-169       1     381 []       3     402 ..       3     402 .. 0.98

  Alignments for each domain:
  == domain 1  score: 550.0 bits;  conditional E-value: 1.3e-169
                        TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk..........lnlpnleklGlgkiee......lagvdave 62 
                                      r+ +++lds+G+G+a+da+ f+d G++t+ghia+a+++          l+lpnl+klGl+ + +       +g  +  
  lcl|FitnessBrowser__PV4:5210370   3 RTVIMMLDSFGVGAAKDAEAFGDTGSNTFGHIAKACAEgkandgregpLKLPNLAKLGLALAAKestgsfAEGFGDDV 80 
                                      6789*********************************99*********************9998899998899999** PP

                        TIGR01696  63 evlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkpasGtvildelGe 136
                                      ev+++y++++e+ssGkdt++Ghwe+aG+++l e+++fs   ++fp+el dk+ erag+  +lgn++asGt+il+elGe
  lcl|FitnessBrowser__PV4:5210370  81 EVIGAYGHADELSSGKDTPSGHWEMAGVPVLYEWGYFSdlkDSFPKELTDKILERAGLSgFLGNCHASGTAILEELGE 158
                                      **************************************9999****************99****************** PP

                        TIGR01696 137 ehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfkrtsnrhdyalk 213
                                      ehm +G +i+ytsadsv+qia+hee+++le+ly lc++are+l    y+iGr+iarpfvG  + +f rt+nr+dya++
  lcl|FitnessBrowser__PV4:5210370 159 EHMTSGLPIFYTSADSVFQIACHEETFGLENLYTLCQIAREELE--PYNIGRVIARPFVGTgPSDFARTGNRKDYAVE 234
                                      ******************************************96..5*************99**************** PP

                        TIGR01696 214 pfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftg.isfanlvdfdalyGhrrdk 290
                                      p++ktvldklk+++ +v+s+Gkiadiy+ +Gitkkv+++++++++d++++++k++++  i+f+n+vdfd+ yGhrrd 
  lcl|FitnessBrowser__PV4:5210370 235 PPSKTVLDKLKEAGGEVVSVGKIADIYAHCGITKKVKATGLEALFDATLEQVKQAGDRtIVFTNFVDFDSHYGHRRDI 312
                                      *********************************************************99******************* PP

                        TIGR01696 291 eGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkvkkgqalesaetfadiGatla 368
                                      +Gya+ale fd+rlpe+l++l e+dll+ltadhG+dpt++Gtdhtre +pvl+y+    +g +l+++++fadiG+++a
  lcl|FitnessBrowser__PV4:5210370 313 AGYARALEYFDSRLPEMLALLGEEDLLLLTADHGCDPTWQGTDHTRERVPVLAYGAGLAPG-SLGRRNSFADIGQSIA 389
                                      *************************************************************.**************** PP

                        TIGR01696 369 dnfntskpeyGks 381
                                       +f+ + +eyG s
  lcl|FitnessBrowser__PV4:5210370 390 SYFGLEPMEYGES 402
                                      ***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (405 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: 9.34
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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