GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Klebsiella michiganensis M5al

Align Histidine transport system permease protein HisM (characterized)
to candidate BWI76_RS10375 BWI76_RS10375 polar amino acid ABC transporter inner membrane subunit

Query= SwissProt::P0AEU3
         (238 letters)



>FitnessBrowser__Koxy:BWI76_RS10375
          Length = 221

 Score =  115 bits (288), Expect = 7e-31
 Identities = 74/229 (32%), Positives = 118/229 (51%), Gaps = 11/229 (4%)

Query: 5   LHEYWK-PLLWTD-GYRFTGVAITLWLLILSVVIGGVLALFLAIGRVSSNKYIQFPIWLF 62
           +H  W   L+W +      G+ +TL L +L+ ++G +L L + + R    ++       F
Sbjct: 1   MHYQWDFSLVWQNLPVLLKGLGVTLELWLLAGIVGTLLGLAVGVVRARGPRFFYPLTSAF 60

Query: 63  TYIFRGTPLYVQLLVFYSGMYTLEIVKGTEFLNAFFRSGLNCTVLALTLNTCAYTTEIFA 122
             +FR TP+ +QL+ FY   Y   ++ G +F      S      LALTL T AY+TEIF 
Sbjct: 61  VEVFRNTPVLIQLIWFY---YAFPVLVGIQF------STFGAAALALTLYTAAYSTEIFR 111

Query: 123 GAIRSVPHGEIEAARAYGFSTFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATV 182
             ++S+  G+ E A+A G     M R IILP   R  LPA +N +I +   T+LA   TV
Sbjct: 112 AGLQSIERGQWEGAKALGMPPGVMLRRIILPQVFRRMLPALTNRMIELAKVTSLASILTV 171

Query: 183 PDLLKIARDINAATYQPFTAFGIAAVLYLIISYVLISLFRRAEKRWLQH 231
            +L+   R +++  Y+P   F + A+LY ++ +    L  R E+R+  H
Sbjct: 172 NELMYQGRLLSSTWYRPVEIFTVVALLYFVLIWPGSYLAARLERRYRPH 220


Lambda     K      H
   0.330    0.142    0.438 

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: 147
Number of extensions: 4
Number of successful extensions: 2
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: 238
Length of database: 221
Length adjustment: 23
Effective length of query: 215
Effective length of database: 198
Effective search space:    42570
Effective search space used:    42570
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 (21.9 bits)
S2: 46 (22.3 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