GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysL in Lactobacillus oryzae SG293

Align L-lysine transport protein (characterized)
to candidate WP_034526228.1 LOSG293_RS01580 arginine-ornithine antiporter

Query= CharProtDB::CH_019644
         (501 letters)



>NCBI__GCF_000740055.1:WP_034526228.1
          Length = 490

 Score =  323 bits (829), Expect = 7e-93
 Identities = 169/474 (35%), Positives = 271/474 (57%), Gaps = 25/474 (5%)

Query: 20  VSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLARRK 79
           +S+  LIAL++GS +G G+F++  ++ + AG GA++IGW+I G+GML +A  F  L  ++
Sbjct: 9   LSLLELIALVVGSIIGGGVFNLMHDMAAGAGAGAIIIGWVITGIGMLMLAKTFQNLTMKR 68

Query: 80  PHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDHPFV 139
           P L++GVY+YA  G G Y+GF+SAWGYWL + +  VGYATL  S + ++ P+F       
Sbjct: 69  PDLEAGVYSYAEAGFGKYMGFNSAWGYWLSAWLGNVGYATLMMSAVAYFFPVFKDGQNIW 128

Query: 140 SALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTVDLW 199
           S LA S + W    ++ RG+  A+F+ T+ T+AK++P+  F++ +  + F    FT   W
Sbjct: 129 SILAASVILWACHFMILRGVESASFVNTIITIAKLIPIFIFLVTM-IIAFRLGVFTSGFW 187

Query: 200 ARDGG---VGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLLL 256
               G     ++  QVR  M+ TVWVFIGIEGA V+S +AR R DV RATV+G + V+L+
Sbjct: 188 YTPSGDFQFSNVMSQVRNTMLVTVWVFIGIEGAVVFSGRARRRKDVGRATVLGIITVILI 247

Query: 257 LVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQMLC 316
              I+ LS GV+ +  LA L   +MA++L++VVG WGA L++ GL +SV+GA++SW M  
Sbjct: 248 YALITLLSLGVMRRAGLAELSQPAMAALLQSVVGKWGAVLVNAGLIISVIGAWLSWTMFA 307

Query: 317 AEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLATN 376
            +     A +G  P      N  GA   +   + I +++F+  + +    Y     +A+ 
Sbjct: 308 GQLPYEAAKEGTFPKIFAKENKNGAPVNSLWFTNICVELFMFSYLITAQAYHFFYSIASA 367

Query: 377 LYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSVW 436
             L+PY FSAFY +  + +         G                 ++ VG+++++Y+VW
Sbjct: 368 AILIPYAFSAFYQLKYSLQEDASVAGRTG-----------------NIWVGVISSIYAVW 410

Query: 437 LFYAAEPQFVLFGAMAMLPGLIPYVW---TRIYRGEQVFNRFEIGVVVVLVVAA 487
           L YAA   ++L  ++    G IP  W    R  + E+VF   E+ V +++ + A
Sbjct: 411 LLYAANLGYILLMSLLFAAG-IPVYWLLQKRDNKAEKVFGPTEMVVAILVALLA 463


Lambda     K      H
   0.327    0.139    0.421 

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: 683
Number of extensions: 41
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 501
Length of database: 490
Length adjustment: 34
Effective length of query: 467
Effective length of database: 456
Effective search space:   212952
Effective search space used:   212952
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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