GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2554 in Klebsiella michiganensis M5al

Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate BWI76_RS10375 BWI76_RS10375 polar amino acid ABC transporter inner membrane subunit

Query= reanno::acidovorax_3H11:Ac3H11_2554
         (222 letters)



>FitnessBrowser__Koxy:BWI76_RS10375
          Length = 221

 Score =  156 bits (394), Expect = 3e-43
 Identities = 80/214 (37%), Positives = 131/214 (61%), Gaps = 2/214 (0%)

Query: 4   DFSPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAI 63
           DFS VW  +P LL G  VT+E+   + ++G ++GL VG+ R    R   Y L +A+V   
Sbjct: 6   DFSLVWQNLPVLLKGLGVTLELWLLAGIVGTLLGLAVGVVRARGPR-FFYPLTSAFVEVF 64

Query: 64  RGTPLLVQLFILFFGLPQF-GILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEA 122
           R TP+L+QL   ++  P   GI    F    + L +Y+ AY +E+ R  +QSI++GQ E 
Sbjct: 65  RNTPVLIQLIWFYYAFPVLVGIQFSTFGAAALALTLYTAAYSTEIFRAGLQSIERGQWEG 124

Query: 123 ARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISV 182
           A+++GM  G+ +R ++LPQ   RM+P L N  I L K ++L S+LT+++LM++G+ + S 
Sbjct: 125 AKALGMPPGVMLRRIILPQVFRRMLPALTNRMIELAKVTSLASILTVNELMYQGRLLSST 184

Query: 183 SYRSLEVYLAIAVVYFILTGATTLVLRRIELRLR 216
            YR +E++  +A++YF+L    + +  R+E R R
Sbjct: 185 WYRPVEIFTVVALLYFVLIWPGSYLAARLERRYR 218


Lambda     K      H
   0.328    0.143    0.412 

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: 135
Number of extensions: 6
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: 222
Length of database: 221
Length adjustment: 22
Effective length of query: 200
Effective length of database: 199
Effective search space:    39800
Effective search space used:    39800
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 (21.8 bits)
S2: 45 (21.9 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