GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Klebsiella michiganensis M5al

Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate BWI76_RS16800 BWI76_RS16800 amino acid ABC transporter permease

Query= SwissProt::P0AER5
         (224 letters)



>FitnessBrowser__Koxy:BWI76_RS16800
          Length = 254

 Score =  129 bits (324), Expect = 5e-35
 Identities = 83/247 (33%), Positives = 126/247 (51%), Gaps = 25/247 (10%)

Query: 1   MYEFDWSSIVPSLPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWF----- 55
           M  F W  I    P  +DG ++T+K T+  V++G LWG  L + R++      W      
Sbjct: 1   MTGFRWEIIEEYGPLFMDGALMTIKCTIICVILGTLWGLTLGLGRMAKAEHGVWKYVLRY 60

Query: 56  -----AKAYVNVFRSIPL-VMVLLWFYLIVPGFLQNVLGLSPKNDIR------------- 96
                 + YV+ FR  PL V +++  + +VP F+    GL   + +              
Sbjct: 61  LVQFPVRFYVSAFRGTPLFVQIMVVHFALVPLFINPRDGLLVTSGMMSADFARELRSNYG 120

Query: 97  -LISAMVAFSMFEAAYYSEIIRAGIQSISRGQSSAALALGMTHWQSMKLIILPQAFRAMV 155
             +S +VA ++   AY SEI RAGIQSI +GQ  A+ ALGM  W++M+ +ILPQAFR ++
Sbjct: 121 AFLSCIVAITLNAGAYVSEIFRAGIQSIDKGQMEASRALGMPWWKTMRQVILPQAFRRIL 180

Query: 156 PLLLTQGIVLFQDTSLVYVLSLADFFRTASTIGERDGTQVEMILFAGFVYFVISLSASLL 215
           P L    I + +D+SL   + LAD    A T+     T  E  L    VY+VI+   + L
Sbjct: 181 PPLGNNAIAIVKDSSLASAIGLADLAYAARTVSGAYATYWEPYLTISLVYWVITFLLAQL 240

Query: 216 VSYLKRR 222
           V+ L++R
Sbjct: 241 VNRLEKR 247


Lambda     K      H
   0.330    0.140    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: 144
Number of extensions: 7
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: 224
Length of database: 254
Length adjustment: 23
Effective length of query: 201
Effective length of database: 231
Effective search space:    46431
Effective search space used:    46431
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