GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rbsC in Klebsiella michiganensis M5al

Align ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate BWI76_RS07650 BWI76_RS07650 ABC transporter permease

Query= TCDB::Q9X050
         (331 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS07650 BWI76_RS07650 ABC
           transporter permease
          Length = 351

 Score =  251 bits (641), Expect = 2e-71
 Identities = 135/319 (42%), Positives = 191/319 (59%), Gaps = 8/319 (2%)

Query: 13  YQRISRYQSIFILLGLIVLFSFLSNRFLTLENFWIILRQTAVNLCIAVGMTFVILTGGID 72
           Y  + + ++   LL +I  FS +   FLT  N  I+ +  A+   +A+GMT VILTGGID
Sbjct: 8   YMYLLKARTFIALLLVIAFFSVMVPNFLTTSNLLIMTQHVAITGLLAIGMTLVILTGGID 67

Query: 73  LSVGSILGFSGAVTAKLLKYGLILSAFGVVLKFNPLGASIIGVLAGFAIGLFNGFIITRF 132
           LSVG++ G  G V   LL  GL L   G V+ FN     +   L G  +G  NG +ITRF
Sbjct: 68  LSVGAVAGICGMVAGALLTNGLPLWN-GSVIFFNVPEVILCVALFGVLVGFVNGAVITRF 126

Query: 133 NIPPFVATLGTMTAVRGFIMLLTKGHPITRLGD-------SFDFIGSGWFLGIPMPVWIA 185
            + PF+ TLG M   RG  +L   G     L          F  +GSG  +GI +P+W+ 
Sbjct: 127 GVAPFICTLGMMYVARGSALLFNDGSTYPNLNGMEALGNTGFSTLGSGTLMGIYLPIWLM 186

Query: 186 AIATGVGIFILRKTQFGRYVYAVGGNEKAAVLSGVNSKLTKLWVYAISGILSAVAGLIVT 245
                +G ++  KT  GRY+YA+GGNE AA L+GV     K++VYA SG+ SA  GLIV 
Sbjct: 187 IGFLLLGYWLTTKTPLGRYIYAIGGNESAARLAGVPIVKAKIFVYAFSGLCSAFVGLIVA 246

Query: 246 ARLDSAQPNAGLMYELDAIAATVIGGASLSGGKGTLIGTVVGALIIGVLNDGLVLVGVSP 305
           ++L +A P  G M+E+DAI ATV+GG +L+GG+G + G+++GA +I  L DG+V++GVS 
Sbjct: 247 SQLQTAHPMTGNMFEMDAIGATVLGGTALAGGRGRVTGSIIGAFVIVFLADGMVMMGVSD 306

Query: 306 FWQQVAKGFIIIAAVIAEK 324
           FWQ V KG +I+ AV+ ++
Sbjct: 307 FWQMVIKGVVIVTAVVVDQ 325


Lambda     K      H
   0.327    0.144    0.427 

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: 412
Number of extensions: 30
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: 331
Length of database: 351
Length adjustment: 28
Effective length of query: 303
Effective length of database: 323
Effective search space:    97869
Effective search space used:    97869
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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