GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysP in Thermoactinomyces daqus H-18

Align lysine-specific permease (characterized)
to candidate WP_033101984.1 JG50_RS0115245 amino acid permease

Query= CharProtDB::CH_003129
         (489 letters)



>NCBI__GCF_000763315.1:WP_033101984.1
          Length = 484

 Score =  635 bits (1639), Expect = 0.0
 Identities = 292/482 (60%), Positives = 387/482 (80%), Gaps = 1/482 (0%)

Query: 5   TKTTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYF 64
           ++   +P L+R LKARHL+MIAIGGSIGTG+F+ASGA+IS+AGPGGAL++Y+ IG+MVYF
Sbjct: 2   SQQNRSPELKRGLKARHLSMIAIGGSIGTGVFLASGASISEAGPGGALVAYLAIGIMVYF 61

Query: 65  LMTSLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWW 124
           LMTSLGE+A +MPV+GSF+TY   +V+   GFA+GWNYWYNWA+TIAV+L A  L+M +W
Sbjct: 62  LMTSLGEMATFMPVAGSFSTYAGRFVDPALGFAMGWNYWYNWAITIAVELSAGSLIMDYW 121

Query: 125 FPDTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKG 184
           FP +P  +WSALFL ++F LN +SV+G+GE+EYWFS IKV TVI+FI++G+LMI GI  G
Sbjct: 122 FPHSPSILWSALFLLLMFGLNALSVKGYGESEYWFSFIKVATVIIFIVIGLLMIFGIM-G 180

Query: 185 AQPAGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQ 244
            +  G+ N+TI +APF  G+  ++ V MI GFSFQGTEL+G+AAGESE+P KN+P+A+RQ
Sbjct: 181 GEAIGFKNFTINDAPFHHGWLGILSVFMIAGFSFQGTELVGVAAGESENPRKNVPKAIRQ 240

Query: 245 VFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVI 304
           VFWRILLFY  AIL++ L++PYT+P+L+  DV  I+ SPFT++F+ AGL  AA+VMNAVI
Sbjct: 241 VFWRILLFYALAILVMGLVLPYTNPNLVGGDVNQIAKSPFTIIFEKAGLAFAASVMNAVI 300

Query: 305 LTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSM 364
           LT+VLSAGNSGMYASTRML+ +A +GKAP++FAK++R GVP  AL  TT +  + FL S+
Sbjct: 301 LTSVLSAGNSGMYASTRMLWQMAKEGKAPKLFAKVNRRGVPVFALLLTTAVGAVAFLASL 360

Query: 365 FGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPIFA 424
            G   +Y+WLLN SG++GFIAWLGIAISHYRFRR YV QG D+N L YR+ +FP GP+FA
Sbjct: 361 VGQGKIYIWLLNASGLSGFIAWLGIAISHYRFRRAYVAQGRDLNHLVYRAKWFPFGPLFA 420

Query: 425 FILCLIITLGQNYEAFLKDTIDWGGVAATYIGIPLFLIIWFGYKLIKGTHFVRYSEMKFP 484
            +LC+I+ +GQNY+AF  +TIDW G+  +YIG+PLF+++W GYK +K T  +   E+   
Sbjct: 421 LVLCVIVIVGQNYQAFTGNTIDWNGILVSYIGLPLFILLWLGYKWVKKTKVIPLKEVDLE 480

Query: 485 QN 486
            N
Sbjct: 481 SN 482


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: 888
Number of extensions: 37
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: 489
Length of database: 484
Length adjustment: 34
Effective length of query: 455
Effective length of database: 450
Effective search space:   204750
Effective search space used:   204750
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