GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Herbaspirillum seropedicae SmR1

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate HSERO_RS08275 HSERO_RS08275 branched-chain amino acid transporter permease subunit LivH

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>FitnessBrowser__HerbieS:HSERO_RS08275
          Length = 308

 Score =  360 bits (923), Expect = e-104
 Identities = 183/299 (61%), Positives = 230/299 (76%), Gaps = 3/299 (1%)

Query: 6   QQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITWV 65
           QQL+NGLSLGAIY LIAIGYTMVYGIIGMINFAHGEIYMI ++V L+T  AIG      +
Sbjct: 10  QQLVNGLSLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIASYVGLVTLTAIGVQSGYPL 69

Query: 66  PLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGAR 125
           PL L   L+ S+L T +YGWTVER+AYRPLR  PRL PLISAIGMSIFLQNYVQI QGAR
Sbjct: 70  PLLLGGALIVSVLVTGLYGWTVERVAYRPLRGGPRLVPLISAIGMSIFLQNYVQIGQGAR 129

Query: 126 SKPLQPILPGNLTLMDGA---VSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQ 182
              +  ++ G L    G+   V++ Y R+  + +T+ LM   T  I R+ +GRA RAC +
Sbjct: 130 DMSVPVLISGALEFQMGSDFTVTIPYSRMVIVGVTLVLMVALTLFIARSRMGRACRACAE 189

Query: 183 DKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLG 242
           D  MA LLG++ ++VIS TFV+GA LAAV G+++ L  G ++ YIGF+AG+KAFTAAVLG
Sbjct: 190 DMGMANLLGIDTNKVISFTFVLGAMLAAVGGVLIALTIGKLNPYIGFIAGIKAFTAAVLG 249

Query: 243 GIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIEKV 301
           GIGS+PGAMLGGV++GL E F +GY+ SE+KDV +F +LVL+L+FRPTGLLG+P++EKV
Sbjct: 250 GIGSIPGAMLGGVLLGLAETFAAGYLPSEYKDVVSFGLLVLILLFRPTGLLGKPDVEKV 308


Lambda     K      H
   0.329    0.144    0.425 

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: 425
Number of extensions: 22
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: 301
Length of database: 308
Length adjustment: 27
Effective length of query: 274
Effective length of database: 281
Effective search space:    76994
Effective search space used:    76994
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 (21.8 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