GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysP in Pseudarthrobacter sulfonivorans Ar51

Align lysine-specific permease (characterized)
to candidate WP_058929813.1 AU252_RS05225 amino acid permease

Query= CharProtDB::CH_003129
         (489 letters)



>NCBI__GCF_001484605.1:WP_058929813.1
          Length = 470

 Score =  263 bits (672), Expect = 1e-74
 Identities = 152/428 (35%), Positives = 234/428 (54%), Gaps = 15/428 (3%)

Query: 8   TEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMT 67
           T    L   LK R LTM+ +G +IG GLF+ SGA I  AGP   L+SY++ G ++  +M 
Sbjct: 7   TSGRALGAALKPRQLTMMGLGSAIGAGLFIGSGAGIQAAGPA-VLISYLVAGTLIILVMW 65

Query: 68  SLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPD 127
           +LGE+AA  P SG+F+ Y         G  +GW +W    V IA + + A  ++S  FP 
Sbjct: 66  ALGEMAAANPDSGAFSVYTAKAYGPVAGATVGWLWWLQLVVVIAAEALGAAGLLSTIFPA 125

Query: 128 TPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKGAQP 187
            P W+ + +F+ V+  +N  SV+ FGE E+WF+L+KV  ++ F++VG  ++ G   G Q 
Sbjct: 126 LPVWLMAFVFIVVLTAVNLTSVKNFGEFEFWFALLKVAAIVGFLLVGAALLFGWLPGVQS 185

Query: 188 AGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFW 247
            G +N+T G+     GFA +     +V F+F GTE++ +AA E+ +PA+++  AVR V W
Sbjct: 186 PGLANFT-GDGFAPDGFAGIATALFVVAFAFGGTEIVSVAAAETAEPARSVRTAVRTVLW 244

Query: 248 RILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTA 307
           RIL+FY+ AI +I+ ++P     L          SPF  V + AG+  AA  +  V + A
Sbjct: 245 RILVFYIGAIFVIAAVVPVGSAGL---------KSPFAAVLEAAGMPGAATAITLVAVAA 295

Query: 308 VLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFGN 367
           +LSA N+ +Y ++RM Y+LA  G+APR+ A +S+  VP  A+ A+     +  +  +   
Sbjct: 296 LLSALNANLYGASRMAYSLADRGEAPRLLASVSKARVPVVAVLASVAFGVVTVVLELAFP 355

Query: 368 QTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPIFA-FI 426
           + V   LLN  G T  + W    ++    R     +G    +LP R   FP    F   I
Sbjct: 356 EKVLPVLLNIVGSTCLLVWTSALLAQLALRLRANREG---TELPLRMPGFPWLTCFGLLI 412

Query: 427 LCLIITLG 434
           L  I T+G
Sbjct: 413 LAAIFTVG 420


Lambda     K      H
   0.327    0.142    0.451 

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: 663
Number of extensions: 46
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: 489
Length of database: 470
Length adjustment: 34
Effective length of query: 455
Effective length of database: 436
Effective search space:   198380
Effective search space used:   198380
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