Alignments for a candidate for deoB in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Shewanella amazonensis SB2B

Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 6936793 Sama_0975 phosphopentomutase (RefSeq)

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



>FitnessBrowser__SB2B:6936793
          Length = 407

 Score =  729 bits (1882), Expect = 0.0
 Identities = 349/404 (86%), Positives = 380/404 (94%)

Query: 1   MKRTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEGKADTGRKGPLALPNLARLG 60
           MKRT+I+MLDSFG+GAA DA KFGDVGSDTFGHIA+ CAEGKA+ GR+G L LPNL+RLG
Sbjct: 1   MKRTIILMLDSFGIGAADDADKFGDVGSDTFGHIAQMCAEGKANNGREGELKLPNLSRLG 60

Query: 61  LAHAAMESTGAFAPGFADNVDLIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH 120
           LAHAA E+TGAFAPGF DNVD+IGAYGH QELSSGKDTPSGHWEMAGVPVLFEWGYFSEH
Sbjct: 61  LAHAAKEATGAFAPGFGDNVDIIGAYGHCQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH 120

Query: 121 QNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQIAC 180
           QNSFPKELTDKIL RAGL  FLGNCHASGTTILEELGEEHM++GKPIFYTSADSVFQIAC
Sbjct: 121 QNSFPKELTDKILERAGLTEFLGNCHASGTTILEELGEEHMKTGKPIFYTSADSVFQIAC 180

Query: 181 HEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAKTV 240
           HE +FGLENLYRLCEIAREELEPYNIGRVIARPF GTGPSDFARTGNR+DY++EPP+KTV
Sbjct: 181 HEESFGLENLYRLCEIAREELEPYNIGRVIARPFVGTGPSDFARTGNRRDYAVEPPSKTV 240

Query: 241 LDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTNFV 300
           LDKLK AGGEVVSVGKI+DIYA+CGITKKVKA+GLE LFDATL ++K AG+NTIVFTNFV
Sbjct: 241 LDKLKQAGGEVVSVGKISDIYAHCGITKKVKASGLEDLFDATLEQIKQAGDNTIVFTNFV 300

Query: 301 DFDSHYGHRRDVAGYAKGLEYFDARLPEMLALLDEDDLLILTADHGCDPTWQGTDHTREY 360
           DFDSHYGHRRDV+GYAK LEYFDARLPE++ALL+E DLL+LTADHGCDPTWQGTDHTRE+
Sbjct: 301 DFDSHYGHRRDVSGYAKALEYFDARLPELMALLEEGDLLLLTADHGCDPTWQGTDHTREF 360

Query: 361 VPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI 404
           VPVLAYGAGL+AGSLG+R SFADIGQSIASYF L  MEYGESF+
Sbjct: 361 VPVLAYGAGLEAGSLGKRGSFADIGQSIASYFGLAAMEYGESFM 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: 735
Number of extensions: 18
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: 407
Length adjustment: 31
Effective length of query: 373
Effective length of database: 376
Effective search space:   140248
Effective search space used:   140248
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 6936793 Sama_0975 (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.30201.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   7.9e-175  567.1   0.0   8.9e-175  567.0   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6936793  Sama_0975 phosphopentomutase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936793  Sama_0975 phosphopentomutase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  567.0   0.0  8.9e-175  8.9e-175       1     381 []       3     402 ..       3     402 .. 0.98

  Alignments for each domain:
  == domain 1  score: 567.0 bits;  conditional E-value: 8.9e-175
                         TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk..........lnlpnleklGlgkiee......lagvdav 61 
                                       r+ +++lds+GiG+a+da++f+d+G+dt+ghia+ +++          l+lpnl++lGl+++ +       +g  ++
  lcl|FitnessBrowser__SB2B:6936793   3 RTIILMLDSFGIGAADDADKFGDVGSDTFGHIAQMCAEgkanngregeLKLPNLSRLGLAHAAKeatgafAPGFGDN 79 
                                       678999******************************9999*********************99989999999***** PP

                         TIGR01696  62 eevlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkpasGtvildel 134
                                        +++++y++ +e+ssGkdt++Ghwe+aG+++l+e+++fs   n+fp+el dk+ erag+  +lgn++asGt+il+el
  lcl|FitnessBrowser__SB2B:6936793  80 VDIIGAYGHCQELSSGKDTPSGHWEMAGVPVLFEWGYFSehqNSFPKELTDKILERAGLTeFLGNCHASGTTILEEL 156
                                       ***************************************9999***************998**************** PP

                         TIGR01696 135 GeehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfkrtsnrhdy 210
                                       GeehmktGk+i+ytsadsv+qia+hee ++le+ly+lce+are+l    y+iGr+iarpfvG  + +f rt+nr dy
  lcl|FitnessBrowser__SB2B:6936793 157 GEEHMKTGKPIFYTSADSVFQIACHEESFGLENLYRLCEIAREELE--PYNIGRVIARPFVGTgPSDFARTGNRRDY 231
                                       ********************************************96..5*************99************* PP

                         TIGR01696 211 alkpfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftg.isfanlvdfdalyGh 286
                                       a++p++ktvldklk+++ +v+s+Gki+diy+ +Gitkkv++ +++d++d++++++k+++++ i+f+n+vdfd+ yGh
  lcl|FitnessBrowser__SB2B:6936793 232 AVEPPSKTVLDKLKQAGGEVVSVGKISDIYAHCGITKKVKASGLEDLFDATLEQIKQAGDNtIVFTNFVDFDSHYGH 308
                                       ***************************************************************************** PP

                         TIGR01696 287 rrdkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkvkkgqalesaetfadi 363
                                       rrd++Gya+ale fdarlpel+++l e dll+ltadhG+dpt++Gtdhtre++pvl+y+     g +l+++ +fadi
  lcl|FitnessBrowser__SB2B:6936793 309 RRDVSGYAKALEYFDARLPELMALLEEGDLLLLTADHGCDPTWQGTDHTREFVPVLAYGAGLEAG-SLGKRGSFADI 384
                                       ***************************************************************99.*********** PP

                         TIGR01696 364 GatladnfntskpeyGks 381
                                       G+++a +f+ + +eyG s
  lcl|FitnessBrowser__SB2B:6936793 385 GQSIASYFGLAAMEYGES 402
                                       ****************86 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.05
//
[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