GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Escherichia coli BW25113

Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 14790 b0653 glutamate and aspartate transporter subunit (NCBI)

Query= TCDB::Q8YPM7
         (381 letters)



>FitnessBrowser__Keio:14790
          Length = 224

 Score =  124 bits (310), Expect = 3e-33
 Identities = 73/210 (34%), Positives = 122/210 (58%), Gaps = 8/210 (3%)

Query: 174 LWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLA 233
           L +GL++TL +   ++V+    G +LA+ R S+   V WF+  Y+ + R +PL+ +L   
Sbjct: 16  LLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIPLVMVLLWF 75

Query: 234 QVMLPLFFAADVRLD-----RVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALG 288
            +++P F    + L      R++ A+    +F AAY +E +R G+Q++SRGQ  AA ALG
Sbjct: 76  YLIVPGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSISRGQSSAALALG 135

Query: 289 LNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIG 348
           +  +  + LI+LPQA RA++P L+ Q I LF+DTSL+ ++ L +    A +I  +    G
Sbjct: 136 MTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRTASTIGERD---G 192

Query: 349 RYAEVYLFIGLIYWLFCYSMSLASRRLERQ 378
              E+ LF G +Y++   S SL    L+R+
Sbjct: 193 TQVEMILFAGFVYFVISLSASLLVSYLKRR 222


Lambda     K      H
   0.332    0.145    0.452 

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: 234
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: 381
Length of database: 224
Length adjustment: 26
Effective length of query: 355
Effective length of database: 198
Effective search space:    70290
Effective search space used:    70290
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: 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