GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Magnetospirillum magneticum AMB-1

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_043743902.1 AMB_RS08455 branched-chain amino acid ABC transporter permease

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



>NCBI__GCF_000009985.1:WP_043743902.1
          Length = 291

 Score =  163 bits (413), Expect = 4e-45
 Identities = 109/304 (35%), Positives = 166/304 (54%), Gaps = 23/304 (7%)

Query: 4   FLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGIT 63
           FLQ L +GL+ GAIY L  +G+ ++Y    +INFA GE  MIG  +A  T +A G     
Sbjct: 5   FLQYLFSGLTSGAIYALAGLGFAIIYNASHVINFAQGEFIMIGG-MATATMVAAGVPIYL 63

Query: 64  WVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQG 123
            +PLA+     ASML     G  +E+ A  P R++  +  +I  IG SIF++   Q++  
Sbjct: 64  AIPLAM----AASMLV----GVAMEKFAIEPARNADVVTIIIITIGASIFMRGAAQLIWD 115

Query: 124 ARSKPLQ------PILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQ 177
                L       PI     TLM  ++ V  +      + IAL++ F     RT  G+A 
Sbjct: 116 KEFHSLPAFSGETPIAVMGATLMPQSLWVFGIS----AVAIALLWYF---FNRTMFGKAM 168

Query: 178 RACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFT 237
                ++  A L+GV V RV+  +F + A L AV G++V  I    ++  G + G+K F+
Sbjct: 169 LGTSHNRLAAQLVGVAVKRVLLASFALSALLGAVGGIVVTPIT-FTNYEAGIMLGLKGFS 227

Query: 238 AAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPE 297
           AAVLGG+G+  GA++GG+++G+ EA  SGY+ S +KD   F I++ VL F P+GL G+  
Sbjct: 228 AAVLGGLGNGTGAIIGGLIVGIAEAMASGYLSSAYKDAIAFIIILFVLFFMPSGLFGKRG 287

Query: 298 IEKV 301
            ++V
Sbjct: 288 TDRV 291


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: 260
Number of extensions: 11
Number of successful extensions: 4
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: 291
Length adjustment: 26
Effective length of query: 275
Effective length of database: 265
Effective search space:    72875
Effective search space used:    72875
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