GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Paraburkholderia bryophila 376MFSha3.1

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate H281DRAFT_04410 H281DRAFT_04410 phosphoglucosamine mutase

Query= SwissProt::Q68BJ6
         (456 letters)



>FitnessBrowser__Burk376:H281DRAFT_04410
          Length = 452

 Score =  194 bits (492), Expect = 6e-54
 Identities = 147/452 (32%), Positives = 220/452 (48%), Gaps = 24/452 (5%)

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

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

Query: 117 GMGLKKEREAIVEELFFSEDFHRAKWNEIGELRK-EDIIKPYIEAIKNRVDVEAIKKRRP 175
           G  L  E E+ +EE         A   ++G+ R+ +D    YIE  K+     A   R  
Sbjct: 124 GNKLPDEVESQIEE-HLELPLACASSEQLGKARRLDDAAGRYIEFCKSTFPA-AFDLRGL 181

Query: 176 FVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALG 235
            +VVD ++GA     P++  ELG +++ +   P+G     N           +  V+A  
Sbjct: 182 KLVVDCAHGAAYDVAPHVFHELGAEIIPIGVAPNGF--NINDGVGATAPDALVRAVRANH 239

Query: 236 ADFGVAQDGDADRAVFIDENGRFIQGDK-TFALVADAVLRENGGGLLVTTIATSNLLDDI 294
           AD G+A DGDADR   +D  GR   GD+  + LV D +  +      V T+ T+  ++  
Sbjct: 240 ADLGIALDGDADRLQVVDAAGRLYNGDELLYVLVKDRIATDGKVEGAVGTLMTNMAVEVA 299

Query: 295 AKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFA 354
            +  G K +R  VGD  V   L E+   +G E +G ++  D     DG ++   ++    
Sbjct: 300 LQAAGVKFVRAAVGDRYVLEQLREHGWQLGAEGSGHILSLDRHSTGDGIVSALLVLAAMK 359

Query: 355 KSGKKFSELIDELPKYYQ--FKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFD 412
           +S K  +EL+D +  + Q     +   + D K   A    +A  +    D  +G      
Sbjct: 360 RSDKTLAELLDGVTLFPQKLINVRMKPDADWKGSDAIRRAIASAE----DALNGR----- 410

Query: 413 DGWVLVRASGTEPIIRIFSEAKSEEKAREYLE 444
            G VL+RASGTEP++R+  EA+  + A  + E
Sbjct: 411 -GRVLIRASGTEPVLRVMVEAEHADDALRHAE 441


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: 31
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.

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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