GapMind for catabolism of small carbon sources

 

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

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate H281DRAFT_00427 H281DRAFT_00427 monosaccharide ABC transporter membrane protein, CUT2 family

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>FitnessBrowser__Burk376:H281DRAFT_00427
          Length = 341

 Score =  223 bits (568), Expect = 5e-63
 Identities = 135/335 (40%), Positives = 199/335 (59%), Gaps = 10/335 (2%)

Query: 9   AASTGAPLPAGTLGRLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASI 68
           +A TG     G   R+ +   L+ L     L+LL + FS  +  F    N+  I Q  ++
Sbjct: 8   SALTGQRRLTGLRARIFSPTALQKLLAFASLILLLVFFSFASPAFMQMDNILGILQATAV 67

Query: 69  NMVLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSLMPQLGM-LSVPAALLCGLLFGIV 127
           N VLA   TFVI+TGGIDLSVG++++ +AV+  +      L M L V AA+  G + G +
Sbjct: 68  NGVLAIASTFVIITGGIDLSVGTLMTFTAVICGVFLTYWHLPMWLGVIAAIGTGAICGTI 127

Query: 128 NGALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDI-GFAFIGNGEVLG------ 180
           +G L A MK+PPFI TLG +  ++GL+ +V  D  IY  D   F  I    ++G      
Sbjct: 128 SGTLTAKMKIPPFIATLGMMLLLKGLSLVVSADKPIYFTDTENFYMISQDSLIGYLVPSL 187

Query: 181 -VPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLL 239
            +P  V+I F +  VS   L RT LG   +A+G N EA RLSG+ V    + +Y + G +
Sbjct: 188 PIPNAVLILFFLAIVSSVTLNRTALGRYTFALGSNEEAVRLSGVNVDRWKIAIYGLGGAI 247

Query: 240 AGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLS 299
            G+ G++ ++RL +A    LGQ YEL+AIAAV++GGTS  GG+G+I+GT++GA I++VL+
Sbjct: 248 CGIAGLLIASRLNSAQPA-LGQGYELEAIAAVVIGGTSLSGGSGTILGTIIGAFIMSVLT 306

Query: 300 NGLVLLGVSDIWQYIIKGLVIIGAVALDSYRRKGS 334
           NGL ++ V+  WQ ++ GL+II AV  D  RR+ S
Sbjct: 307 NGLRIMSVAQEWQIVVTGLIIILAVYADILRRRKS 341


Lambda     K      H
   0.325    0.141    0.409 

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: 367
Number of extensions: 25
Number of successful extensions: 5
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: 337
Length of database: 341
Length adjustment: 28
Effective length of query: 309
Effective length of database: 313
Effective search space:    96717
Effective search space used:    96717
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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