GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Azospirillum brasilense Sp245

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate AZOBR_RS07040 AZOBR_RS07040 phosphoglucosamine mutase

Query= SwissProt::Q68BJ6
         (456 letters)



>FitnessBrowser__azobra:AZOBR_RS07040
          Length = 455

 Score =  222 bits (565), Expect = 2e-62
 Identities = 154/447 (34%), Positives = 229/447 (51%), Gaps = 34/447 (7%)

Query: 4   LFGTFGVRGIAN-EEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDALI 62
           LFGT G+RG AN + +T E AL++ MA   L  R G  R  VV+G+DTR+SG +L+ AL 
Sbjct: 5   LFGTDGIRGTANIDPMTAETALRVAMA-SALQFRRGDHRHRVVIGKDTRLSGYLLEPALT 63

Query: 63  SGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKK 122
           +G +S G DV+ +G  PTPA+   T    AD G +I+ASHNP + NGIKL  P+G  L  
Sbjct: 64  AGFISMGMDVVLLGPLPTPAVAMLTRSLRADLGVMISASHNPYQDNGIKLFGPDGYKLSD 123

Query: 123 EREAIVE---------ELFFSEDFHRAKWNEIGELRKEDIIKPYIEAIKNRVDVEAIKKR 173
             E  +E         +L  S D  RA        R ED    YIE +KN      ++  
Sbjct: 124 AVELAIETRMGQPFAPDLAGSADLGRAS-------RLEDSTGRYIEYVKNTFP-RGLRLD 175

Query: 174 RPFVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKA 233
              +VVD +NGA     P +L ELG  V+ V  +PDG     N +      +   E V A
Sbjct: 176 GLRIVVDCANGAAYRVAPKVLYELGADVIPVGVNPDG--LNINKDCGATATRTLQEQVVA 233

Query: 234 LGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVAD--AVLRENGGGLLVTTIATSNLL 291
            GA  G+A DGDADR + +DE GR + GD+  AL+A   A  +   GG +V T+ ++  +
Sbjct: 234 HGAHLGIALDGDADRLIMVDEAGRVVDGDQVMALIASSWAQAQTLKGGGVVATVMSNLGM 293

Query: 292 DDIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVE 351
           +   +  G  ++RT VGD  V   + E+   +GGE++G V+  D+    DG +   +++ 
Sbjct: 294 ERHLQGLGIALVRTPVGDRYVVEHMREHGYNVGGEQSGHVVLSDYSTTGDGLIAALQVLA 353

Query: 352 IFAKSGKKFSELIDEL--PKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKI 409
           +  +SG + +  + ++  P   +    R   G +   +A V         +    DG   
Sbjct: 354 VLIQSGGRAASEVCQVFAPVPQKLTNVRFAAGSKPLEIASV---------QAAIRDGEAR 404

Query: 410 IFDDGWVLVRASGTEPIIRIFSEAKSE 436
           +   G +L+R SGTEP+IR+ +E   E
Sbjct: 405 LNGSGRILIRKSGTEPVIRVMAEGDDE 431


Lambda     K      H
   0.317    0.139    0.396 

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: 507
Number of extensions: 28
Number of successful extensions: 6
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: 456
Length of database: 455
Length adjustment: 33
Effective length of query: 423
Effective length of database: 422
Effective search space:   178506
Effective search space used:   178506
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