GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoB in Azospirillum brasilense Sp245

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate AZOBR_RS07040 AZOBR_RS07040 phosphoglucosamine mutase

Query= BRENDA::Q6I7B6
         (450 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS07040 AZOBR_RS07040
           phosphoglucosamine mutase
          Length = 455

 Score =  155 bits (391), Expect = 3e-42
 Identities = 144/446 (32%), Positives = 214/446 (47%), Gaps = 41/446 (9%)

Query: 3   LFGTAGIRGTL-WEKVTPELAMKVGMAVGT-YKSG----KALVGRDGRTSSVMLKNAMIS 56
           LFGT GIRGT   + +T E A++V MA    ++ G    + ++G+D R S  +L+ A+ +
Sbjct: 5   LFGTDGIRGTANIDPMTAETALRVAMASALQFRRGDHRHRVVIGKDTRLSGYLLEPALTA 64

Query: 57  GLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDG------ 109
           G +S GM+V+    +PTPA+A  TR L AD GVMI+ASHNP  DNG+K+F  DG      
Sbjct: 65  GFISMGMDVVLLGPLPTPAVAMLTRSLRADLGVMISASHNPYQDNGIKLFGPDGYKLSDA 124

Query: 110 TEFYVEQERG---LEEIIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVL 166
            E  +E   G     ++  S +  +A   E    R +E + +     L   G    L+++
Sbjct: 125 VELAIETRMGQPFAPDLAGSADLGRASRLEDSTGRYIEYVKNTFPRGLRLDG----LRIV 180

Query: 167 YDGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDL 226
            D ANGA   VAP +L E+GA V+ V  + DG       +        L + V   G  L
Sbjct: 181 VDCANGAAYRVAPKVLYELGADVIPVGVNPDG--LNINKDCGATATRTLQEQVVAHGAHL 238

Query: 227 AIAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEH--GGGTVVVSIDTGSRIDAVVE 284
            IA DGDADR+ + DE G  VD D V+AL A  + +     GG VV ++ +   ++  ++
Sbjct: 239 GIALDGDADRLIMVDEAGRVVDGDQVMALIASSWAQAQTLKGGGVVATVMSNLGMERHLQ 298

Query: 285 RAGGRVVRIPLGQPH--DGIKRY-KAIFAAEPWKLVHPKFGPWIDPFV-TMGLLIKLIDE 340
             G  +VR P+G  +  + ++ +   +   +   +V   +    D  +  + +L  LI  
Sbjct: 299 GLGIALVRTPVGDRYVVEHMREHGYNVGGEQSGHVVLSDYSTTGDGLIAALQVLAVLIQS 358

Query: 341 NGPLSELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIAL 400
            G  +  V            V  P   K   VR AA     +++S       I      L
Sbjct: 359 GGRAASEV----------CQVFAPVPQKLTNVRFAAGSKPLEIAS---VQAAIRDGEARL 405

Query: 401 NDGSWILIRPSGTEPKIRVVAEAPTE 426
           N    ILIR SGTEP IRV+AE   E
Sbjct: 406 NGSGRILIRKSGTEPVIRVMAEGDDE 431


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: 484
Number of extensions: 28
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 450
Length of database: 455
Length adjustment: 33
Effective length of query: 417
Effective length of database: 422
Effective search space:   175974
Effective search space used:   175974
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