GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacG in Klebsiella michiganensis M5al

Align LacG, component of Lactose porter (characterized)
to candidate BWI76_RS17835 BWI76_RS17835 sugar ABC transporter permease

Query= TCDB::P29824
         (273 letters)



>FitnessBrowser__Koxy:BWI76_RS17835
          Length = 279

 Score =  137 bits (345), Expect = 3e-37
 Identities = 82/278 (29%), Positives = 148/278 (53%), Gaps = 10/278 (3%)

Query: 5   LRRRLPDIVQYSVLSLAAFLSIFPFIWMVIGTTNTTSQIIRGKVTFGTALFDNIASFFAQ 64
           L +R     ++ + +L   + + PF W ++ T  + + +  G++      F      FA 
Sbjct: 2   LSKRWDTAGRWCIYALLLIVFVGPF-WGIVATAFSGAPVKPGELLAWPNQFSFENFIFAW 60

Query: 65  VDVPL--VFWNSVKIALVGTALTLLVSSLAGYGFEMFRSKLRERVYTVILLTLMVPFAAL 122
           +D+ +     NS+ +   GT L + VS+LA Y     + +    V  VIL T+M+P   +
Sbjct: 61  MDIGVWQYLLNSILVVFFGTVLQVSVSALAAYALARKKFRGVALVSLVILSTMMLPEEVI 120

Query: 123 MIPLFMLMG------QAGLLNTHIAIMLPMIASAFIIFYFRQASKAFPTELRDAAKVDGL 176
            IPL+M++        A L N+++ ++LP++  AF IF   +   A P EL +AA++DG 
Sbjct: 121 AIPLYMIINWRLPFIDASLYNSYLGMILPVVGWAFSIFVLTEFMSAIPKELEEAARIDGA 180

Query: 177 KEWQIFFYIYVPVMRSTYAAAFVIVFMLNWNNYLWPLIVLQSNDTKTITLVVSSLASAYS 236
            EWQIFF++ +P+++          F++ W+ YL PLIV+  +   TI +++ +L +  S
Sbjct: 181 NEWQIFFHVILPLVKPALGTVVTFGFIMIWDQYLLPLIVVNQDSLNTIPVILGTLRTDES 240

Query: 237 PEYGTVMIGTILATLPTLLVFFAMQRQFVQG-MLGSVK 273
                 +  T+LA LP+++V+  +Q+ F +G M G+VK
Sbjct: 241 ITPNIFIAITLLAMLPSIIVYLGLQKHFNRGIMSGAVK 278


Lambda     K      H
   0.331    0.140    0.416 

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: 263
Number of extensions: 11
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: 273
Length of database: 279
Length adjustment: 25
Effective length of query: 248
Effective length of database: 254
Effective search space:    62992
Effective search space used:    62992
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 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