GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatP in Klebsiella michiganensis M5al

Align Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate BWI76_RS00280 BWI76_RS00280 ribose ABC transporter permease

Query= TCDB::B8H230
         (332 letters)



>FitnessBrowser__Koxy:BWI76_RS00280
          Length = 321

 Score =  236 bits (603), Expect = 4e-67
 Identities = 135/314 (42%), Positives = 193/314 (61%), Gaps = 9/314 (2%)

Query: 16  RFDLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILI 75
           R+   A+  + ++++ LL+L+A+    +  F T  N  NIL + S+  I+AVGMT VIL 
Sbjct: 10  RYFTKAWLMEQKSLIALLVLIAIVSTMSPNFFTVNNLFNILQQTSVNAIMAVGMTLVILT 69

Query: 76  GGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHV 135
            GID++VGSLLA     AA +V   V       L+A+  +  +G A G V G  V    V
Sbjct: 70  SGIDLSVGSLLALTGAVAASIVGIEVNA-----LVAVAAALALGAAIGAVTGVIVAKGRV 124

Query: 136 PAFIVTLGGMTVWRGATLLLNDGGPIS-GFND---AYRWWGSGEILFLPVPVVIFALVAA 191
            AFI TL  M + RG T++  +G P++ GF D    + W+G G  L +P PV I A+V  
Sbjct: 125 QAFIATLVMMLLLRGVTMVYTNGSPVNTGFTDNADLFGWFGIGRPLGIPTPVWIMAIVFL 184

Query: 192 AGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGS 251
           A    L +TR GR +YA+GGN  A RLSG++V+ +   VY++ G LA L+G +  ARL S
Sbjct: 185 AAWYMLHHTRLGRYIYALGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVARLSS 244

Query: 252 AEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQV 311
           A+  AGTGYEL  IA+VV+GG SL GG G + GT++GAL++G L+NGL +L V+SY Q +
Sbjct: 245 AQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMI 304

Query: 312 VIGLIIVAAVAFDH 325
           V  ++I+ AV  D+
Sbjct: 305 VKAVVILLAVLVDN 318


Lambda     K      H
   0.325    0.140    0.413 

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: 260
Number of extensions: 12
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: 332
Length of database: 321
Length adjustment: 28
Effective length of query: 304
Effective length of database: 293
Effective search space:    89072
Effective search space used:    89072
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: 48 (23.1 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