GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltK in Herbaspirillum seropedicae SmR1

Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate HSERO_RS00315 HSERO_RS00315 amino acid ABC transporter permease

Query= SwissProt::P0AER5
         (224 letters)



>FitnessBrowser__HerbieS:HSERO_RS00315
          Length = 250

 Score =  126 bits (316), Expect = 4e-34
 Identities = 81/239 (33%), Positives = 123/239 (51%), Gaps = 20/239 (8%)

Query: 4   FDWSSIVPSLPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAP----------VA 53
           F W  I   LP  ++G  +TLK  +  V+ G  WG +L V RL+              V 
Sbjct: 5   FQWEIIGEYLPLFVEGTWMTLKAAIICVIAGTCWGLVLGVGRLAEARHGFWKYFLCYCVQ 64

Query: 54  WFAKAYVNVFRSIPL-VMVLLWFYLIVPGFLQNVLGLSPKNDIR---------LISAMVA 103
           W  + YV+  R  PL V +LL  + ++P  +    GL    D+            SA++A
Sbjct: 65  WPIRFYVSFLRGTPLFVQILLIHFALMPMLINPSGGLILSGDLAREIRSHYGAFASAVLA 124

Query: 104 FSMFEAAYYSEIIRAGIQSISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGI 163
            ++   AY SEI RAGIQSI RGQS A+ +LGM++  +++ ++LPQAFR M+P L    I
Sbjct: 125 ITLNSGAYVSEIFRAGIQSIDRGQSEASRSLGMSYLATLRRVVLPQAFRRMLPPLGNNAI 184

Query: 164 VLFQDTSLVYVLSLADFFRTASTIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKRR 222
            + +D+SL   + LA+    A T+        E  L    +Y++I+L+ S LV +L+ R
Sbjct: 185 AIVKDSSLASAIGLAELAYAARTVSGAYARYWEPYLTISVIYWLITLALSALVRHLEAR 243


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: 134
Number of extensions: 7
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: 224
Length of database: 250
Length adjustment: 23
Effective length of query: 201
Effective length of database: 227
Effective search space:    45627
Effective search space used:    45627
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