GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natG in Herbaspirillum seropedicae SmR1

Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate HSERO_RS21620 HSERO_RS21620 amino acid ABC transporter permease

Query= TCDB::Q8YPM8
         (308 letters)



>FitnessBrowser__HerbieS:HSERO_RS21620
          Length = 247

 Score =  120 bits (301), Expect = 3e-32
 Identities = 69/227 (30%), Positives = 129/227 (56%), Gaps = 22/227 (9%)

Query: 82  GLINSLRIAFVGIILTTIVGILAGIARLSD------NWLVRNISLV---YVEIFRNTPLL 132
           G++ +L+++ + I++ T++G+L G+ RL++       W ++++  +   YV  FR TPL 
Sbjct: 18  GVLMTLQVSLISILIGTVIGLLVGMLRLAEVQHGPWKWPLKSMRWLAGFYVAFFRGTPLF 77

Query: 133 LQLLFWYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYT---G 189
           +Q++  +FAV   L + ++ + + G +            T   ++ A L G +  +   G
Sbjct: 78  VQIMLIHFAVMPVLVQQEHGLLITGELAR----------TIKQDYGAFLSGTVALSLNAG 127

Query: 190 AFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNS 249
           A+I+EI R GIQS+ +GQ  A  SLG+N  L MR V+ PQA R ++PPL ++ + L K+S
Sbjct: 128 AYISEIFRAGIQSIERGQSYAAASLGMNYGLTMRYVVLPQAFRRMLPPLGNEAITLLKDS 187

Query: 250 SLAIAIGYPDIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIM 296
           SL  AIG  ++ + A T      +  E  + + + Y S+++ ++L++
Sbjct: 188 SLVSAIGLAELAYAARTVAGTYARYWEPYITISVLYFSMTICLALVV 234


Lambda     K      H
   0.328    0.143    0.430 

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: 169
Number of extensions: 10
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: 308
Length of database: 247
Length adjustment: 25
Effective length of query: 283
Effective length of database: 222
Effective search space:    62826
Effective search space used:    62826
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: 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