GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5404 in Rhizorhabdus wittichii RW1

Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit

Query= reanno::pseudo6_N2E2:Pf6N2E2_5404
         (365 letters)



>NCBI__GCF_000016765.1:WP_012048835.1
          Length = 374

 Score = 94.7 bits (234), Expect = 3e-24
 Identities = 75/232 (32%), Positives = 119/232 (51%), Gaps = 39/232 (16%)

Query: 157 GLMLT---LVIATVGIVG-ALPLGIVLALGRRSNMPAIRVVCVTFIEFWRG-------VP 205
           GL LT   + + TVGI G ALP+ IV  LG          + +T I  WRG         
Sbjct: 154 GLFLTNRGITVTTVGITGTALPM-IVTVLGG---------LTLTLITAWRGHLHKASLCT 203

Query: 206 LITVLFMSSVMLPLFLP--------EGMNFD-------KLLRALIGVILFQSAYIAEVVR 250
           L T++  S++ + L L         +  NF        + +  L G +++ SA+ AE+VR
Sbjct: 204 LGTIVAGSALWIVLDLGLARDVPHFDRFNFTGGLTLTPEFVAVLWGSVIYASAFAAEIVR 263

Query: 251 GGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGL 310
           GGL  +P+GQ+EA+ A+GL   +S+ LVI+PQAL++++P + + FI + K+++L +++G 
Sbjct: 264 GGLDGVPRGQWEASRALGLSKRQSLRLVIVPQALRMIVPPMNSQFITILKNSTLALVVGY 323

Query: 311 FDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTG 362
            D LN V   A +    G   EG     LVF+     +S     L  ++  G
Sbjct: 324 PD-LNFVANTAIN--HTGQGLEGVAILMLVFFTLASAISLAMNRLNARVQRG 372



 Score = 32.7 bits (73), Expect = 2e-05
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 148 DAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLI 207
           D +A +   GL  ++ +  + IV +   G+ +AL R S     R +   F++  R VPL+
Sbjct: 69  DTIAWAFVVGLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLV 128

Query: 208 T-VLFMSSVMLPLFLP 222
             +LF   V+L  F P
Sbjct: 129 VQLLFWYGVILMAFPP 144


Lambda     K      H
   0.330    0.144    0.469 

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: 418
Number of extensions: 26
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 365
Length of database: 374
Length adjustment: 30
Effective length of query: 335
Effective length of database: 344
Effective search space:   115240
Effective search space used:   115240
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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