GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS07040
          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 (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