GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Burkholderia phytofirmans PsJN

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate BPHYT_RS16825 BPHYT_RS16825 C4-dicarboxylate ABC transporter

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__BFirm:BPHYT_RS16825
          Length = 441

 Score =  433 bits (1114), Expect = e-126
 Identities = 211/411 (51%), Positives = 305/411 (74%), Gaps = 1/411 (0%)

Query: 6   FKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGME 65
           F SL+ +V+ A+  GI++G  +P   + ++PLGDGF+KLIKM+I P++FC VV+G+A   
Sbjct: 5   FNSLFGRVVIALVAGIVVGAVFPHFAQSLRPLGDGFLKLIKMVIGPIVFCVVVSGMAHAG 64

Query: 66  SMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAK 125
            ++ VGR G  A++YFE+++TIAL+IG I+  V +PG GMN+D  +LD  +++ Y + AK
Sbjct: 65  DLRKVGRVGLKAVIYFEVMTTIALVIGAILAYVTRPGVGMNIDLHSLDPASLSTYTEHAK 124

Query: 126 D-QGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQV 184
             +    F++ +IP + I AFA+G+ILQ+L+F+VLFG AL  LG+K Q + ++I+  SQV
Sbjct: 125 SLKDTAGFLLKIIPDTAINAFATGDILQILVFSVLFGSALSLLGNKAQRVSSLIDELSQV 184

Query: 185 IFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKA 244
            F ++  I++LAP+G  GA+AFT G YGV +L QLG L++ FY++C +FVV+VLG + + 
Sbjct: 185 FFRVMGFIIKLAPLGVLGAIAFTTGTYGVESLKQLGMLVLVFYLSCFVFVVVVLGVVMRL 244

Query: 245 TGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDG 304
            GFSIFK IRY+REEL IVLGT+SS++ LP+++ K+E +G + S VGLVIPTGYSFNLDG
Sbjct: 245 AGFSIFKLIRYLREELSIVLGTASSDAVLPQIMRKLEWMGVKDSTVGLVIPTGYSFNLDG 304

Query: 305 TSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 364
            SIYLT+A +FIAQATN+ + +   I +++V L++SKGA G+ GS  ++LAATLSA+  +
Sbjct: 305 FSIYLTLAVIFIAQATNTPLSVHDLIVVVLVSLVTSKGAHGIPGSAIVILAATLSAIPAI 364

Query: 365 PVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLN 415
           PV GL LIL +D F+  ARALTNL+GN VAT+VVA W  ++D  +   VLN
Sbjct: 365 PVLGLVLILPVDWFVGIARALTNLIGNCVATVVVAVWENDIDRARAHRVLN 415


Lambda     K      H
   0.327    0.142    0.401 

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: 582
Number of extensions: 37
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: 428
Length of database: 441
Length adjustment: 32
Effective length of query: 396
Effective length of database: 409
Effective search space:   161964
Effective search space used:   161964
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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