GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Burkholderia phytofirmans PsJN

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate BPHYT_RS14155 BPHYT_RS14155 phosphoglucosamine mutase

Query= BRENDA::Q6I7B6
         (450 letters)



>FitnessBrowser__BFirm:BPHYT_RS14155
          Length = 452

 Score =  149 bits (376), Expect = 2e-40
 Identities = 149/485 (30%), Positives = 227/485 (46%), Gaps = 77/485 (15%)

Query: 2   RLFGTAGIRGTLWE-KVTPELAMKVGMAVGTYKSGK-----------ALVGRDGRTSSVM 49
           R FGT GIRG + E  +TPE  +++G A G   +G             L+G+D R S  M
Sbjct: 4   RYFGTDGIRGKVGEGPITPEFVLRLGYAAGKVLAGADRWAKSGTRPTVLIGKDTRVSGYM 63

Query: 50  LKNAMISGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGD 108
           L+ A+ SG  + G++V+ A  +PTP +A+ TR L   AGV+I+ASHNP  DNG+K F+ D
Sbjct: 64  LEAALESGFSAAGVDVMLAGPMPTPGIAYLTRALRLAAGVVISASHNPYYDNGIKFFSAD 123

Query: 109 GTEFYVEQERGLEEII-------FSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHET 161
           G +   E E  +EE +        S    KAR  +    R +E       A  D  G   
Sbjct: 124 GNKLPDEVESQIEEQLDLPLACAASEQLGKARRLDDAAGRYIEFCKSTFPAAFDLHG--- 180

Query: 162 NLKVLYDGANGAGSLVAPYLLREMGAKVLSVNA-----HVDGHFPGRKPEPRYENIAYLG 216
            LK++ D A+GA   VAP++  E+GA+V+ +       +++       P+        L 
Sbjct: 181 -LKLVVDCAHGAAYDVAPHVFHELGAEVIPIGVAPNGFNINDGVGATAPDA-------LV 232

Query: 217 KLVRELGVDLAIAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHGG-GTVVVSIDT 275
           + VR    DL IA DGDADR+ V D  G   + D ++ +  K  V   G     V ++ T
Sbjct: 233 RAVRANHADLGIALDGDADRLQVVDAAGRLYNGDELLYILVKDRVATDGKVDGAVGTLMT 292

Query: 276 GSRIDAVVERAGGRVVRIPLGQPHDGIKRYKAIFAAE-PWKLVHPKFGPWI--------D 326
              ++  ++ AG + VR  +G       RY      E  W+L     G  +        D
Sbjct: 293 NMAVEVALQEAGVKFVRAAVGD------RYVLEQLREHGWQLGAEGSGHILSLDRHSTGD 346

Query: 327 PFVTMGLLIKLIDEN-GPLSELVKEIPTYYLKKANV-LCPD-EYK-AEVVRRAAEEVERK 382
             V+  L++  +  +   L++L+  +  +  K  NV + PD ++K ++ +RRA  + E  
Sbjct: 347 GIVSALLVLAAMKRSEKTLADLLDGVTLFPQKLINVRMKPDADWKSSDAIRRAIAKAES- 405

Query: 383 LSSEIKEVLTISGFRIALNDGSWILIRPSGTEPKIRVVAEAPTEKRRDELFEMAYSTVSR 442
                           ALN    +LIR SGTEP +RV+ EA  E   D L      +++ 
Sbjct: 406 ----------------ALNGRGRVLIRASGTEPVLRVMVEA--ENAADAL--QYAESIAG 445

Query: 443 IVKEA 447
            VKEA
Sbjct: 446 AVKEA 450


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: 498
Number of extensions: 24
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: 452
Length adjustment: 33
Effective length of query: 417
Effective length of database: 419
Effective search space:   174723
Effective search space used:   174723
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