Align lysine-specific permease (characterized)
to candidate WP_084937109.1 HA51_RS22655 amino acid permease
Query= CharProtDB::CH_003129 (489 letters) >NCBI__GCF_002095475.1:WP_084937109.1 Length = 488 Score = 860 bits (2222), Expect = 0.0 Identities = 416/484 (85%), Positives = 457/484 (94%) Query: 1 MVSETKTTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGL 60 M +++KTT+ PGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSY LIGL Sbjct: 1 MHNDSKTTQQPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYALIGL 60 Query: 61 MVYFLMTSLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLV 120 MVYFLMTSLGELAA+MPVSGSFATYG YVEEGFGFALGWNYWYNWAVTIAVDLVA+QLV Sbjct: 61 MVYFLMTSLGELAAFMPVSGSFATYGSKYVEEGFGFALGWNYWYNWAVTIAVDLVASQLV 120 Query: 121 MSWWFPDTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIG 180 M++WFPDTPGWIWSALFL ++FLLNYISV+GFGEAEYWFSLIKV TV++FI+VGVLMI G Sbjct: 121 MNYWFPDTPGWIWSALFLCLMFLLNYISVKGFGEAEYWFSLIKVVTVVIFIVVGVLMITG 180 Query: 181 IFKGAQPAGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPR 240 I +GA+ AGW NWT+G+APFAGGFAAMIGVAMIVGFSFQGTELIGIAAGES+DPAKNIPR Sbjct: 181 IMRGAENAGWHNWTVGDAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESQDPAKNIPR 240 Query: 241 AVRQVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVM 300 AVRQVFWRILLFY+FAILIISLI+PYTDP LL NDV DI++SPFTLVFQ+AGLLSAAAVM Sbjct: 241 AVRQVFWRILLFYIFAILIISLILPYTDPKLLHNDVTDIAISPFTLVFQNAGLLSAAAVM 300 Query: 301 NAVILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCF 360 NAVILTAVLSAGNSGMYASTRML+ LA +GKAPRIF KLS+GGVPRNAL ATTV+AGLCF Sbjct: 301 NAVILTAVLSAGNSGMYASTRMLFNLAREGKAPRIFGKLSKGGVPRNALIATTVVAGLCF 360 Query: 361 LTSMFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLG 420 L+S FGNQ VYLWLLNTSGMTGFIAWLGIAISHYRFRRGYV QG ++ DLPYRSGFFPLG Sbjct: 361 LSSKFGNQEVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVAQGLNLADLPYRSGFFPLG 420 Query: 421 PIFAFILCLIITLGQNYEAFLKDTIDWGGVAATYIGIPLFLIIWFGYKLIKGTHFVRYSE 480 PIFAF+LCLIITLGQNY+AFL+D IDW GVAATYIGIPLFL+IW GYKL++G+ +V+YSE Sbjct: 421 PIFAFVLCLIITLGQNYQAFLQDRIDWYGVAATYIGIPLFLLIWLGYKLVRGSRWVKYSE 480 Query: 481 MKFP 484 M+FP Sbjct: 481 MEFP 484 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: 1013 Number of extensions: 36 Number of successful extensions: 1 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: 488 Length adjustment: 34 Effective length of query: 455 Effective length of database: 454 Effective search space: 206570 Effective search space used: 206570 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.
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:
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