GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natC in Frankia alni ACN14a

Align NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_041938756.1 FRAAL_RS03130 branched-chain amino acid ABC transporter permease

Query= TCDB::P74455
         (372 letters)



>NCBI__GCF_000058485.1:WP_041938756.1
          Length = 515

 Score = 88.2 bits (217), Expect = 5e-22
 Identities = 49/121 (40%), Positives = 70/121 (57%), Gaps = 9/121 (7%)

Query: 9   LITSAATYGIFALGLNLQWGFAGLINFGHVAFMTLGAYATTLL-SLRGLPI-------PL 60
           ++     Y + ALGLN+  G+AGL++ G++AF  +GAYAT    S   +P        P 
Sbjct: 201 MVNDIGIYALLALGLNVVVGYAGLLDLGYIAFFAIGAYATAYFTSQTAMPWHAPFVLNPF 260

Query: 61  AVL-VGMGLAMALGLLIGTSTLRLREDYLAIVTIGVSELIRLIANNEEWLTQGTFGVQSF 119
            V  + + LA   G+++G  TLRLR DYLAIVT+G  E+I L+ANN + +T G  G    
Sbjct: 261 FVFPIALVLAALAGVILGAPTLRLRGDYLAIVTLGFGEIIHLVANNADGITNGARGAFGV 320

Query: 120 P 120
           P
Sbjct: 321 P 321



 Score = 67.4 bits (163), Expect = 8e-16
 Identities = 48/155 (30%), Positives = 77/155 (49%), Gaps = 15/155 (9%)

Query: 209 MLLALTL-LALTYAGLEFWVHSPWGRILKAIREDEEIPRALGKNVFWYKLQAFMGGGAIA 267
           +LLA+ + + + +  LE    S  GR   AIREDE    A G      KL AF  G +++
Sbjct: 344 LLLAIVIGVMIAFGRLE---RSRIGRSWAAIREDEIAAEATGVATLRMKLLAFAIGASVS 400

Query: 268 GLAGALFAWQLTSIYPSNFDTLLTFNAWIIVVLGGAGSNAGTVLGTIIFWAYDSLTRFLL 327
           G AG LFA       P +F    +F    +V+ GG GS  G V+G ++      L  +L 
Sbjct: 401 GFAGVLFA-SKQFFNPQSFSLQASFFVVAVVIFGGMGSRLGVVVGAVVL---QGLAFYLR 456

Query: 328 PQIAFLDQSQAGALRVMVIGLILMVLMVWRPQGIL 362
            ++   D       R +  G +++++M++RPQG++
Sbjct: 457 DKVQPAD-------RYIYFGAVIVIMMIFRPQGLV 484



 Score = 25.4 bits (54), Expect = 0.004
 Identities = 38/137 (27%), Positives = 58/137 (42%), Gaps = 17/137 (12%)

Query: 1   MNFGYLIFLITSAATYGIFALGLNLQWGFAGLINFGHVAFMTLGA-YATTLLSLRGLPIP 59
           + FG +I L+ + A          +  G  G     H++   LG  Y   +  L    + 
Sbjct: 294 LGFGEIIHLVANNAD--------GITNGARGAFGVPHLSIDLLGIDYKWGIDPLPYYYLL 345

Query: 60  LAVLVGMGLAMALGLL----IGTSTLRLREDYLAIVTIGVSEL-IRLIANNEEWLTQGTF 114
           LA+++G+   +A G L    IG S   +RED +A    GV+ L ++L+A        G  
Sbjct: 346 LAIVIGV--MIAFGRLERSRIGRSWAAIREDEIAAEATGVATLRMKLLAFAIGASVSGFA 403

Query: 115 GVQSFPWPMDFNPTLLS 131
           GV  F     FNP   S
Sbjct: 404 GV-LFASKQFFNPQSFS 419


Lambda     K      H
   0.327    0.143    0.442 

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: 406
Number of extensions: 19
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 372
Length of database: 515
Length adjustment: 32
Effective length of query: 340
Effective length of database: 483
Effective search space:   164220
Effective search space used:   164220
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 (21.7 bits)
S2: 51 (24.3 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