GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Burkholderia phytofirmans PsJN

Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate BPHYT_RS04470 BPHYT_RS04470 phosphoglucomutase

Query= BRENDA::P26276
         (463 letters)



>FitnessBrowser__BFirm:BPHYT_RS04470
          Length = 464

 Score =  508 bits (1307), Expect = e-148
 Identities = 253/461 (54%), Positives = 337/461 (73%), Gaps = 10/461 (2%)

Query: 12  SIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQG 71
           SIF+AYDIRGV+G TL A+ A  IGRA GSE  A+G   V V RDGRLSGPELV+ L  G
Sbjct: 5   SIFKAYDIRGVIGKTLDADAARSIGRAFGSEVRAQGGDAVVVARDGRLSGPELVQALSDG 64

Query: 72  LVDCGCQVSDVGMVPTPVLYYAANV---LEG-----KSGVMLTGSHNPPDYNGFKIVVAG 123
           L + G  V +VGMVPTPV Y+AA+V   L+G      S +++TGSHNPPDYNGFK+V+ G
Sbjct: 65  LREAGVDVVNVGMVPTPVGYFAASVPLQLDGGERRVDSCIVVTGSHNPPDYNGFKMVLRG 124

Query: 124 ETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGV 183
             +  EQI AL +RI   + ++G G+  + DI   Y ++I  DI +A+P+K+VVD GNGV
Sbjct: 125 AAIYGEQILALHQRIVDENFSTGSGTYTEYDIADAYLERITSDIKLARPIKIVVDTGNGV 184

Query: 184 AGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDG 243
           AG +AP+L + LGC ++ L+ E+DGNFPNHHPDP  PENL+D+I  +K  +A++G AFDG
Sbjct: 185 AGGLAPKLFKKLGCELVELFTEIDGNFPNHHPDPAHPENLQDVIRALKETDAEIGFAFDG 244

Query: 244 DGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVM 303
           DGDR+GVVT  G IIYPDR LMLFA++V+SRN GA II+DVKCTR L   +   GG P+M
Sbjct: 245 DGDRLGVVTKDGEIIYPDRQLMLFAEEVLSRNKGAQIIYDVKCTRNLAKWVKDKGGEPLM 304

Query: 304 WKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHV 363
           WKTGHSL+K K++ETGA LAGEMSGHVFFK+RW+GFDDG+Y+ ARLLEIL++ + D   +
Sbjct: 305 WKTGHSLVKAKLRETGAPLAGEMSGHVFFKDRWYGFDDGLYTGARLLEILTRVE-DPSKL 363

Query: 364 FSAFPSDISTPEINITVTEDSKFAIIEALQRDAQW-GEGNITTLDGVRVDYPKGWGLVRA 422
            ++ P+  STPE+ + + E   F +I  LQ++A++ G  ++  +DG+RV+YP G+GL R+
Sbjct: 364 LNSLPNSNSTPELQLKLEEGENFELIARLQQNAKFTGADDVVKIDGLRVEYPDGFGLARS 423

Query: 423 SNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463
           SNTTPV+V+RFEAD +  L+RI+  FR  + A      +PF
Sbjct: 424 SNTTPVVVMRFEADNDAALKRIQEDFRRVIMAEKPDAKLPF 464


Lambda     K      H
   0.319    0.138    0.410 

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: 627
Number of extensions: 21
Number of successful extensions: 3
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: 463
Length of database: 464
Length adjustment: 33
Effective length of query: 430
Effective length of database: 431
Effective search space:   185330
Effective search space used:   185330
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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