GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24005 in Escherichia coli BW25113

Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate 16415 b2308 histidine/lysine/arginine/ornithine transporter subunit (NCBI)

Query= uniprot:B2TBJ7
         (240 letters)



>FitnessBrowser__Keio:16415
          Length = 228

 Score =  163 bits (413), Expect = 2e-45
 Identities = 84/223 (37%), Positives = 138/223 (61%), Gaps = 1/223 (0%)

Query: 13  GWGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELL 72
           G+ GV+L  AL+T+ L ++++ +  + G + A  KLS+ R   +I + YTT+ RGVP+L+
Sbjct: 4   GFSGVILQGALVTLELAISSVVLAVIIGLIGAGGKLSQNRLSGLIFEGYTTLIRGVPDLV 63

Query: 73  VIYLFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVSRG 132
           ++ L ++G    + +V +  G  G + + P V G + +G I GAY  E +R A +AV +G
Sbjct: 64  LMLLIFYGLQIALNTVTEAMGV-GQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPKG 122

Query: 133 ELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTSQV 192
            +EAA + G     + RRI+ P ++R+ALPGIGN WQ+ LK +AL+S+ GL ++++ +Q+
Sbjct: 123 HIEAATAFGFTRGQVFRRIMFPSMMRYALPGIGNNWQVILKSTALVSLLGLEDVVKATQL 182

Query: 193 AAGSTHQYFTFFVVGGALYLIMTSISNRVFNRAEAHVGRSFKR 235
           A  ST + F F +V G +YL+ T++SN V    E       KR
Sbjct: 183 AGKSTWEPFYFAIVCGVIYLVFTTVSNGVLLFLERRYSVGVKR 225


Lambda     K      H
   0.327    0.141    0.403 

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: 121
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: 240
Length of database: 228
Length adjustment: 23
Effective length of query: 217
Effective length of database: 205
Effective search space:    44485
Effective search space used:    44485
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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