GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Klebsiella michiganensis M5al

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>FitnessBrowser__Koxy:BWI76_RS14865
          Length = 339

 Score =  270 bits (690), Expect = 4e-77
 Identities = 146/299 (48%), Positives = 205/299 (68%), Gaps = 1/299 (0%)

Query: 33  LGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSI 92
           +G+L VL++L I  S    NF    NL  IA+  S+N +LAAGMTFVILT GIDLSVGSI
Sbjct: 25  VGILIVLLVLLILMSTFAPNFNRVDNLLNIARSISVNAILAAGMTFVILTSGIDLSVGSI 84

Query: 93  LSISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRG 152
           +++S VV+++ ++      L++ A +  G L G++NG L A++ L PFIVTLGT+T +RG
Sbjct: 85  VAVSGVVSVVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPFIVTLGTMTFLRG 144

Query: 153 LARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVG 212
           +A  +     I +  + F  +GNG ++G+P  VII   V  ++WF+L RT  G  IYAVG
Sbjct: 145 MAYTITEGQPIVSSSLSFRELGNGYLIGIPIPVIIMLVVYLLAWFILERTRFGRHIYAVG 204

Query: 213 GNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVI 272
           GNA+AARL+G++V  VL  VY ++G+ AGL G++ +AR+ +A     G  YELDAIAAV+
Sbjct: 205 GNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQP-TAGTGYELDAIAAVV 263

Query: 273 LGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSYRR 331
           LGGTS  GG G I+GTL+G++I+ VLS GL+LL V    Q +IKG+VII AVA+D  ++
Sbjct: 264 LGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIVIILAVAIDGLKQ 322


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: 368
Number of extensions: 20
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: 337
Length of database: 339
Length adjustment: 28
Effective length of query: 309
Effective length of database: 311
Effective search space:    96099
Effective search space used:    96099
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