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.30507.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.83
//
[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:

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:

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:

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:

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