GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livM in Magnetospirillum magneticum AMB-1

Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate WP_011385249.1 AMB_RS14460 branched-chain amino acid ABC transporter permease

Query= SwissProt::P22729
         (425 letters)



>lcl|NCBI__GCF_000009985.1:WP_011385249.1 AMB_RS14460 branched-chain
           amino acid ABC transporter permease
          Length = 329

 Score =  145 bits (365), Expect = 2e-39
 Identities = 104/322 (32%), Positives = 161/322 (50%), Gaps = 28/322 (8%)

Query: 91  LFLVALLVLAVAW-PFMVSRGTVDIA---TLTMIYIILGLGLNVVVGLSGLLVLGYGGFY 146
           L L+A L L  AW P   S     +    T  MI  IL + L+++VG++GL+ LG+  F+
Sbjct: 13  LVLLAALALFPAWGPLAFSAKYAFLLQKLTGIMILAILAMSLDLLVGVAGLVSLGHAAFF 72

Query: 147 AIGAYTFALLN-HYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIV 205
            +G Y  ALL+  Y     W  LP A    AA   ++GF  +R  G Y  +VTL FG++ 
Sbjct: 73  GLGGYMLALLSPQYEAANAWVVLPAAMGAVAAVSAVVGFLAIRTAGIYFIMVTLAFGQM- 131

Query: 206 RILLLNNTEITGGPNGISQIPKPTL--FGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIF 263
                N++++ GG +G     KP +  FG+                   +  +      F
Sbjct: 132 GYYFFNDSKLAGGSDGAYIYVKPNVEAFGITL-----------------VNLESKQAFFF 174

Query: 264 LYLVALLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFA 323
           + L  L+ V L L V+   L  P GR   A+  +E   R LG +P   KL AF ++ A A
Sbjct: 175 VVLGCLVAVYLWLRVV---LASPFGRVLAAIGVNEGRVRGLGFNPMVYKLVAFALAGALA 231

Query: 324 GFAGTLFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFN 383
           G AG L A + GFVSP    + +S  VL +V+LGGMG+ F  +L A +L ++   +    
Sbjct: 232 GLAGFLAATQYGFVSPAMLGWHQSGHVLVMVILGGMGTLFGPVLGAFILELAHFGLEAVT 291

Query: 384 EYSMLMLGGLMVLMMIWRPQGL 405
           E+ +L +G L++ +++  P+G+
Sbjct: 292 EHWLLPMGVLVITIVLALPKGV 313


Lambda     K      H
   0.330    0.145    0.436 

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: 341
Number of extensions: 14
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: 425
Length of database: 329
Length adjustment: 30
Effective length of query: 395
Effective length of database: 299
Effective search space:   118105
Effective search space used:   118105
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: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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