GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoB in Desulfovibrio vulgaris Hildenborough

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 206109 DVU0685 phosphomannomutase

Query= BRENDA::Q6I7B6
         (450 letters)



>lcl|MicrobesOnline__882:206109 DVU0685 phosphomannomutase
          Length = 453

 Score =  189 bits (481), Expect = 1e-52
 Identities = 148/457 (32%), Positives = 224/457 (49%), Gaps = 26/457 (5%)

Query: 3   LFGTAGIRGTLWEKVTPELAMKVGMAVGTY----KSGKALVGRDGRTSSVMLKNAMISGL 58
           +F    IRG +     PE   ++G A GTY      G A+VG D R SS    +A++ GL
Sbjct: 8   VFRAYDIRGIVDTDFDPEWVERLGRACGTYFVSHGHGAAVVGFDCRHSSPAYHDALVRGL 67

Query: 59  LSTGMEVLDADLIPTPALAWGTRKLA-DAGVMITASHNPPTDNGVKVFNGDGTEFYVEQE 117
           LSTG++V    ++PTP L +  + L   AGVMITASHNP   NG KV  G+ T  + E+ 
Sbjct: 68  LSTGVDVTSVGMVPTPVLYFAVKHLGRKAGVMITASHNPSEYNGFKVVAGEST-IHGEEI 126

Query: 118 RGLEEIIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYDGANGAGSLV 177
           R + E+   G F              +++P YI A+   V     LKV+ DG NGAG  +
Sbjct: 127 RRIWEVFERGEFASGHGIGCSH----DIVPSYIEAITSDVHPARKLKVVVDGGNGAGGEL 182

Query: 178 APYLLREMGAKVLSVNAHVDGHFPGRKPEPRYE-NIAYLGKLVRELGVDLAIAQDGDADR 236
              +LR +G +V++     DG FP   P+P  E N+  L + V+    DL I  DGDADR
Sbjct: 183 CVEVLRRLGVEVVAQFCEPDGDFPNHHPDPVVEANMTALMERVQVERADLGIGLDGDADR 242

Query: 237 IAVFDEKGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAGGRVVRIPLG 296
           +   D  G  ++ D +++L+A+  +    G TV+  +    R+   +E  GG+ +    G
Sbjct: 243 LGAVDGMGRLLNGDELLSLYAREMLARRPGETVIADVKCSHRLFDDIEAHGGKPMMWITG 302

Query: 297 QPHDGIK-RYKAIFAAEPWKLV-HPKFGP-WI---DPFVTMGLLIKLIDENG-PLSELVK 349
             H  +K R   + A    +L  H  FG  W    D       L++L+  +  PL++L  
Sbjct: 303 --HSVVKARMLEVGAPLAGELSGHMFFGDRWFGFDDAIYGAARLVELLAASDVPLTDLPG 360

Query: 350 EIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIALNDGSWILIR 409
             P++  ++ ++ CP+  K EVVRRA      + +     +  I G R+   DG W L+R
Sbjct: 361 WPPSHATRELHLPCPEHAKFEVVRRAQAYFRERCT-----INDIDGARVIFPDG-WGLVR 414

Query: 410 PSGTEPKIRVVAEAPTEKRRDELFEMAYSTVSRIVKE 446
            S T+P + +  EA T +R  E+       + R V E
Sbjct: 415 ASNTQPVLVLRFEAQTPERLAEIRAFVEEPLRRWVAE 451


Lambda     K      H
   0.318    0.138    0.402 

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: 489
Number of extensions: 21
Number of successful extensions: 7
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: 450
Length of database: 453
Length adjustment: 33
Effective length of query: 417
Effective length of database: 420
Effective search space:   175140
Effective search space used:   175140
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 (21.6 bits)
S2: 51 (24.3 bits)

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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