Alignments for a candidate for deoB in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Dinoroseobacter shibae DFL-12

Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 3607415 Dshi_0829 phosphopentomutase (RefSeq)

Query= reanno::Dino:3607415
         (399 letters)



>FitnessBrowser__Dino:3607415
          Length = 399

 Score =  814 bits (2103), Expect = 0.0
 Identities = 399/399 (100%), Positives = 399/399 (100%)

Query: 1   MTRAFLIVMDSVGCGGAPDAADFGDEGANTLAHIAQACAAGRADAGRSGPLRMPVLDGLG 60
           MTRAFLIVMDSVGCGGAPDAADFGDEGANTLAHIAQACAAGRADAGRSGPLRMPVLDGLG
Sbjct: 1   MTRAFLIVMDSVGCGGAPDAADFGDEGANTLAHIAQACAAGRADAGRSGPLRMPVLDGLG 60

Query: 61  LGAAIRLASGAETPGLAATPTGLWGAATEVSRGKDTPTGHWELAGVPVPWEWTTFPDTDP 120
           LGAAIRLASGAETPGLAATPTGLWGAATEVSRGKDTPTGHWELAGVPVPWEWTTFPDTDP
Sbjct: 61  LGAAIRLASGAETPGLAATPTGLWGAATEVSRGKDTPTGHWELAGVPVPWEWTTFPDTDP 120

Query: 121 AFPPDLLAEMARAAGTEGTLCNTHASGTEVIERFGAEHLRTGWPICYTSVDSVLQIAAHE 180
           AFPPDLLAEMARAAGTEGTLCNTHASGTEVIERFGAEHLRTGWPICYTSVDSVLQIAAHE
Sbjct: 121 AFPPDLLAEMARAAGTEGTLCNTHASGTEVIERFGAEHLRTGWPICYTSVDSVLQIAAHE 180

Query: 181 EAFGLDRLLDVCETLAPRLHAMKVGRVIARPFLGSEATGFARTQNRRDFAIAPPAPTLCD 240
           EAFGLDRLLDVCETLAPRLHAMKVGRVIARPFLGSEATGFARTQNRRDFAIAPPAPTLCD
Sbjct: 181 EAFGLDRLLDVCETLAPRLHAMKVGRVIARPFLGSEATGFARTQNRRDFAIAPPAPTLCD 240

Query: 241 RVQAAGRRVHAIGKIKDIFSGRGIDTVAKGSDAALMEALIAAGQVAEEGSLTFANFVEFD 300
           RVQAAGRRVHAIGKIKDIFSGRGIDTVAKGSDAALMEALIAAGQVAEEGSLTFANFVEFD
Sbjct: 241 RVQAAGRRVHAIGKIKDIFSGRGIDTVAKGSDAALMEALIAAGQVAEEGSLTFANFVEFD 300

Query: 301 SLYGHRRDVAGYARALEWFDAQLPRFLATLRPGDLAIFTADHGNDPTWHGTEHTRERVPV 360
           SLYGHRRDVAGYARALEWFDAQLPRFLATLRPGDLAIFTADHGNDPTWHGTEHTRERVPV
Sbjct: 301 SLYGHRRDVAGYARALEWFDAQLPRFLATLRPGDLAIFTADHGNDPTWHGTEHTRERVPV 360

Query: 361 VGYGVGVHEVGIVGFRDVGATIGAHLGVEMFDMGKAMLP 399
           VGYGVGVHEVGIVGFRDVGATIGAHLGVEMFDMGKAMLP
Sbjct: 361 VGYGVGVHEVGIVGFRDVGATIGAHLGVEMFDMGKAMLP 399


Lambda     K      H
   0.321    0.137    0.429 

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: 733
Number of extensions: 20
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: 399
Length of database: 399
Length adjustment: 31
Effective length of query: 368
Effective length of database: 368
Effective search space:   135424
Effective search space used:   135424
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate 3607415 Dshi_0829 (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.11974.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.3e-124  401.8   0.0   1.5e-124  401.6   0.0    1.0  1  lcl|FitnessBrowser__Dino:3607415  Dshi_0829 phosphopentomutase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607415  Dshi_0829 phosphopentomutase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.6   0.0  1.5e-124  1.5e-124       1     381 []       3     396 ..       3     396 .. 0.93

  Alignments for each domain:
  == domain 1  score: 401.6 bits;  conditional E-value: 1.5e-124
                         TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk..........lnlpnleklGlgkieela.gvda...vee 63 
                                       r+fliv+dsvG G a+daadf+deGa+tl hia+a++           l++p l+ lGlg +  la g ++   ++ 
  lcl|FitnessBrowser__Dino:3607415   3 RAFLIVMDSVGCGGAPDAADFGDEGANTLAHIAQACAAgradagrsgpLRMPVLDGLGLGAAIRLAsGAETpglAAT 79 
                                       89***********************************99********************998774413433222689 PP

                         TIGR01696  64 vlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkpasGtvildelGe 136
                                       + + ++ + e+s Gkdt+tGhwe+aG+++  e+  f+    +fp +ll ++ + ag +  l+n++asGt +++++G 
  lcl|FitnessBrowser__Dino:3607415  80 PTGLWGAATEVSRGKDTPTGHWELAGVPVPWEWTTFPdtdPAFPPDLLAEMARAAGTEgTLCNTHASGTEVIERFGA 156
                                       9************************************66668**************999****************** PP

                         TIGR01696 137 ehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfkrtsnrhdyal 212
                                       eh++tG +i yts dsvlqiaahee ++l++l ++ce+    l+    ++Gr+iarpf+G  a  f rt+nr d+a+
  lcl|FitnessBrowser__Dino:3607415 157 EHLRTGWPICYTSVDSVLQIAAHEEAFGLDRLLDVCETLAPRLHA--MKVGRVIARPFLGSeATGFARTQNRRDFAI 231
                                       **************************************9999876..569**********8799************* PP

                         TIGR01696 213 kpfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftg.isfanlvdfdalyGhrr 288
                                        p+a+t+ d+++ ++  v +iGki+di++g Gi    +  s  ++++++i   + + +g ++fan+v+fd+lyGhrr
  lcl|FitnessBrowser__Dino:3607415 232 APPAPTLCDRVQAAGRRVHAIGKIKDIFSGRGIDTVAK-GSDAALMEALIAAGQVAEEGsLTFANFVEFDSLYGHRR 307
                                       *********************************76555.68899******9999888888***************** PP

                         TIGR01696 289 dkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkvkkgqalesaetfadiGa 365
                                       d++Gya+ale fda+lp +l+ lr  dl i+tadhGndpt++Gt+htre +pv+ y+  v +   +     f d+Ga
  lcl|FitnessBrowser__Dino:3607415 308 DVAGYARALEWFDAQLPRFLATLRPGDLAIFTADHGNDPTWHGTEHTRERVPVVGYGVGVHEVGIV----GFRDVGA 380
                                       **********************************************************99988555....5778888 PP

                         TIGR01696 366 tladnfntskpeyGks 381
                                       t+  +++++  + Gk+
  lcl|FitnessBrowser__Dino:3607415 381 TIGAHLGVEMFDMGKA 396
                                       8888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (399 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: 7.72
//
[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