Alignments for a candidate for deoB in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Sinorhizobium meliloti 1021

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate SMc04119 SMc04119 phosphopentomutase

Query= BRENDA::P0A6K6
         (407 letters)



>FitnessBrowser__Smeli:SMc04119
          Length = 406

 Score =  471 bits (1213), Expect = e-137
 Identities = 233/408 (57%), Positives = 299/408 (73%), Gaps = 5/408 (1%)

Query: 1   MKRAFIMVLDSFGIGATEDAERFGDVGADTLGHIAEACAKGEADNG--RKGPLNLPNLTR 58
           M RAF+ VLDSFGIG   DAE FGD+GADTLGHIAE CA G AD    R+GPL+LPN++ 
Sbjct: 1   MARAFLFVLDSFGIGNAPDAEAFGDLGADTLGHIAEFCAAGAADRAGLREGPLHLPNMSA 60

Query: 59  LGLAKAHEGSTGFIPAGMDGNAEVIGAYAWAHEMSSGKDTPSGHWEIAGVPVLFEWGYFS 118
           LGL  A   +TG +PAGM     V G Y  A E+S GKDTPSGHWEIAG PV F+WGYF 
Sbjct: 61  LGLMHAARLATGRLPAGMALPERVYGIYGAASEVSRGKDTPSGHWEIAGTPVTFDWGYFP 120

Query: 119 DHENSFPQELLDKLVERANLPGYLGNCHSSGTVILDQLGEEHMKTGKPIFYTSADSVFQI 178
              ++FP EL++ +    ++PG LGNCH+SGT I+ + GEEHM++GKPI YTS+DSVFQI
Sbjct: 121 AEGDAFPPELVEAICREGDVPGILGNCHASGTDIIARHGEEHMRSGKPICYTSSDSVFQI 180

Query: 179 ACHEETFGLDKLYELCEIAREELTNGGYNIGRVIARPFIGDKAGNFQRTGNRHDLAVEPP 238
           A HE+TFGL++L  LCE+ R  + +  YNIGRVIARPF+G   G+F RTGNR D +V PP
Sbjct: 181 AAHEQTFGLERLLNLCEVVRRLVDD--YNIGRVIARPFVGSDPGSFTRTGNRRDYSVLPP 238

Query: 239 APTVLQKLVDEKHGQVVSVGKIADIYANCGITKKVKATGLDALFDATIKEMKEAGDNTIV 298
            PTVL +L  E    V ++GKI DI+A+ G+T+  KA G  ALFDA+++ ++EA D  +V
Sbjct: 239 EPTVLDRL-QEAGRTVHAIGKIGDIFAHQGVTRLTKANGNMALFDASLEAIEEAEDGALV 297

Query: 299 FTNFVDFDSSWGHRRDVAGYAAGLELFDRRLPELMSLLRDDDILILTADHGCDPTWTGTD 358
           FTNFVDFD  +GHRRDV+GYAA LE FD RLP+L   L+  D++ILTADHGCDPTW GTD
Sbjct: 298 FTNFVDFDMLYGHRRDVSGYAAALEAFDARLPDLDRRLKPGDMVILTADHGCDPTWRGTD 357

Query: 359 HTREHIPVLVYGPKVKPGSLGHRETFADIGQTLAKYFGTSDMEYGKAM 406
           HTRE +PVL++GP ++  S G  ++FA IG+T+A++ G     +G+++
Sbjct: 358 HTRERVPVLMFGPTLRSRSFGIADSFAHIGETVARHLGIGVGPHGRSL 405


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: 633
Number of extensions: 35
Number of successful extensions: 4
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: 406
Length adjustment: 31
Effective length of query: 376
Effective length of database: 375
Effective search space:   141000
Effective search space used:   141000
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 SMc04119 SMc04119 (phosphopentomutase)
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.29459.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.4e-152  491.5   0.0   8.3e-152  491.4   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc04119  SMc04119 phosphopentomutase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc04119  SMc04119 phosphopentomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  491.4   0.0  8.3e-152  8.3e-152       1     379 [.       3     402 ..       3     404 .. 0.97

  Alignments for each domain:
  == domain 1  score: 491.4 bits;  conditional E-value: 8.3e-152
                           TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk............lnlpnleklGlgkiee......lag 57 
                                         r+fl+vlds+GiG+a+da+ f+d Gadtlghiae ++             l+lpn++ lGl ++        +ag
  lcl|FitnessBrowser__Smeli:SMc04119   3 RAFLFVLDSFGIGNAPDAEAFGDLGADTLGHIAEFCAAgaadraglregpLHLPNMSALGLMHAARlatgrlPAG 77 
                                         89**********************************999**********************9999989999999* PP

                           TIGR01696  58 vdaveevlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkpasGt 128
                                         +   e+v + y+ +se+s Gkdt++GhweiaG ++++++++f+   ++fp el++ + +  + + +lgn++asGt
  lcl|FitnessBrowser__Smeli:SMc04119  78 MALPERVYGIYGAASEVSRGKDTPSGHWEIAGTPVTFDWGYFPaegDAFPPELVEAICREGDVPgILGNCHASGT 152
                                         *******************************************99999***************99********** PP

                           TIGR01696 129 vildelGeehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfk 202
                                          i+ + Geehm++Gk+i yts+dsv+qiaahe++++le+l +lce++r l+ d  y+iGr+iarpfvG  +G f+
  lcl|FitnessBrowser__Smeli:SMc04119 153 DIIARHGEEHMRSGKPICYTSSDSVFQIAAHEQTFGLERLLNLCEVVRRLVDD--YNIGRVIARPFVGSdPGSFT 225
                                         *************************************************9976..*************88***** PP

                           TIGR01696 203 rtsnrhdyalkpfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftg.isfan 276
                                         rt+nr dy++ p+++tvld+l++++  v +iGki di++ +G+t+  ++++nm+++d+ ++ ++e+ +g ++f+n
  lcl|FitnessBrowser__Smeli:SMc04119 226 RTGNRRDYSVLPPEPTVLDRLQEAGRTVHAIGKIGDIFAHQGVTRLTKANGNMALFDASLEAIEEAEDGaLVFTN 300
                                         *********************************************************************9***** PP

                           TIGR01696 277 lvdfdalyGhrrdkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkvkkg 351
                                         +vdfd lyGhrrd++Gyaaale fdarlp+l  +l+  d++iltadhG+dpt++Gtdhtre +pvl+++p  ++ 
  lcl|FitnessBrowser__Smeli:SMc04119 301 FVDFDMLYGHRRDVSGYAAALEAFDARLPDLDRRLKPGDMVILTADHGCDPTWRGTDHTRERVPVLMFGPTLRSR 375
                                         ***********************************************************************9987 PP

                           TIGR01696 352 qalesaetfadiGatladnfntskpeyG 379
                                          +++ a++fa+iG+t+a ++++    +G
  lcl|FitnessBrowser__Smeli:SMc04119 376 -SFGIADSFAHIGETVARHLGIGVGPHG 402
                                         .****************99987665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (406 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.70
//
[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