GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Burkholderia phytofirmans PsJN

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate BPHYT_RS14155 BPHYT_RS14155 phosphoglucosamine mutase

Query= SwissProt::Q68BJ6
         (456 letters)



>FitnessBrowser__BFirm:BPHYT_RS14155
          Length = 452

 Score =  195 bits (495), Expect = 3e-54
 Identities = 148/463 (31%), Positives = 223/463 (48%), Gaps = 28/463 (6%)

Query: 3   KLFGTFGVRGIANE-EITPEFALKIGMAFGTLLKREGR-----ERPLVVVGRDTRVSGEM 56
           + FGT G+RG   E  ITPEF L++G A G +L    R      RP V++G+DTRVSG M
Sbjct: 4   RYFGTDGIRGKVGEGPITPEFVLRLGYAAGKVLAGADRWAKSGTRPTVLIGKDTRVSGYM 63

Query: 57  LKDALISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPN 116
           L+ AL SG  + G DV+  G  PTP I + T       G VI+ASHNP   NGIK    +
Sbjct: 64  LEAALESGFSAAGVDVMLAGPMPTPGIAYLTRALRLAAGVVISASHNPYYDNGIKFFSAD 123

Query: 117 GMGLKKEREAIVEELFFSEDFHRAKWNEIGELRK-EDIIKPYIEAIKN----RVDVEAIK 171
           G  L  E E+ +EE         A   ++G+ R+ +D    YIE  K+      D+  +K
Sbjct: 124 GNKLPDEVESQIEEQ-LDLPLACAASEQLGKARRLDDAAGRYIEFCKSTFPAAFDLHGLK 182

Query: 172 KRRPFVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIV 231
                +VVD ++GA     P++  ELG +V+ +   P+G     N           +  V
Sbjct: 183 -----LVVDCAHGAAYDVAPHVFHELGAEVIPIGVAPNGF--NINDGVGATAPDALVRAV 235

Query: 232 KALGADFGVAQDGDADRAVFIDENGRFIQGDK-TFALVADAVLRENGGGLLVTTIATSNL 290
           +A  AD G+A DGDADR   +D  GR   GD+  + LV D V  +      V T+ T+  
Sbjct: 236 RANHADLGIALDGDADRLQVVDAAGRLYNGDELLYILVKDRVATDGKVDGAVGTLMTNMA 295

Query: 291 LDDIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIV 350
           ++   +  G K +R  VGD  V   L E+   +G E +G ++  D     DG ++   ++
Sbjct: 296 VEVALQEAGVKFVRAAVGDRYVLEQLREHGWQLGAEGSGHILSLDRHSTGDGIVSALLVL 355

Query: 351 EIFAKSGKKFSELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKII 410
               +S K  ++L+D +  + Q      ++ D        A+       +         +
Sbjct: 356 AAMKRSEKTLADLLDGVTLFPQKLINVRMKPD--------ADWKSSDAIRRAIAKAESAL 407

Query: 411 FDDGWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEA 453
              G VL+RASGTEP++R+  EA++   A +Y E     ++EA
Sbjct: 408 NGRGRVLIRASGTEPVLRVMVEAENAADALQYAESIAGAVKEA 450


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: 545
Number of extensions: 27
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: 452
Length adjustment: 33
Effective length of query: 423
Effective length of database: 419
Effective search space:   177237
Effective search space used:   177237
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.

Links

Downloads

Related tools

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