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_011385948.1 AMB_RS18170 branched-chain amino acid ABC transporter permease

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



>NCBI__GCF_000009985.1:WP_011385948.1
          Length = 297

 Score =  151 bits (382), Expect = 2e-41
 Identities = 97/305 (31%), Positives = 170/305 (55%), Gaps = 22/305 (7%)

Query: 5   LQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVA--LITFLAIGSLGI 62
           LQ L+NGL +G +YG++A+ + ++Y    ++NFA GE  +IGA+    L+T +A      
Sbjct: 7   LQLLVNGLIVGTLYGVVAMCFVLIYKSTQVVNFAQGEFLLIGAWTCWWLVTSMA------ 60

Query: 63  TWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQ 122
               L   V    + LF  V+G  ++ I  RPL   P ++ ++  IG+SIF Q  ++ + 
Sbjct: 61  ----LPFYVAFPMTFLFMMVFGIALQMIVLRPLIGEPVISVIMVTIGLSIFFQAVMKSIF 116

Query: 123 GARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQ 182
           G  ++P   I P     + G +SV    L ++V++I +M  F      + +G A RA   
Sbjct: 117 GVWAQPFPEIFPVKSVDILG-LSVQPAYLMSLVVSIVIMGLFAWFFKYSRMGLAMRATAF 175

Query: 183 DKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLG 242
           ++++A  LG++V  V +  + + A ++A+AG++V ++ GV      F  G+K F A ++G
Sbjct: 176 NQQVAQSLGISVKAVFATAWAISAMVSALAGVVVGMVNGVSSALSFF--GIKVFPAVIVG 233

Query: 243 GIGSLPGAMLGGVVIGLIEAFWSGYMGSEW------KDVATFTILVLVLIFRPTGLLGRP 296
           G+ S+ GA+LGG++IG++E   + Y   ++        VA F +LV++L+ +P GL G  
Sbjct: 234 GLDSIIGAVLGGLIIGVLENL-AEYADGQYLHLGNLYTVAPFYVLVIILMIKPYGLFGTK 292

Query: 297 EIEKV 301
            IE+V
Sbjct: 293 TIERV 297


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: 295
Number of extensions: 15
Number of successful extensions: 5
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: 297
Length adjustment: 27
Effective length of query: 274
Effective length of database: 270
Effective search space:    73980
Effective search space used:    73980
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