Align lysine-specific permease (characterized)
to candidate WP_084935844.1 HA51_RS17310 proline-specific permease ProY
Query= CharProtDB::CH_003129 (489 letters) >NCBI__GCF_002095475.1:WP_084935844.1 Length = 451 Score = 261 bits (668), Expect = 3e-74 Identities = 150/395 (37%), Positives = 221/395 (55%), Gaps = 18/395 (4%) Query: 9 EAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTS 68 E L+R L RH+ +A+G +IGTGLF S I AGP LL+Y++ G + Y +M + Sbjct: 3 ETNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPS-VLLAYIIGGAIAYIIMRA 61 Query: 69 LGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDT 128 LGE++ P + SF+ Y Q+Y+ G+ GW Y + + D+ A + M WFP+ Sbjct: 62 LGEMSVNNPQASSFSRYAQDYLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPEV 121 Query: 129 PGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMII-GIFKGAQP 187 P WIW + +I +N +SV+ FGE E+WFS KV T+I+ I+ G +I GI G QP Sbjct: 122 PHWIWVLSVVLIIGGINLMSVKVFGEVEFWFSFFKVATIIIMILAGFGIIFWGIGNGGQP 181 Query: 188 AGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFW 247 G N FA G M+ +V F++ G E+IGI AGE+EDPAK+IPRA+ V Sbjct: 182 TGIHNLWSNGGFFAHGIVGMLLSLQMVMFAYGGIEIIGITAGEAEDPAKSIPRAINSVPL 241 Query: 248 RILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTA 307 RIL+FYV + +I I P+ N V SPF L FQH G+ +AA+++N V++TA Sbjct: 242 RILVFYVGTLFVIMSIYPW-------NQV-GTQGSPFVLTFQHLGIAAAASLLNFVVITA 293 Query: 308 VLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFGN 367 LSA NS ++ RML+ +A G AP++F S G P + T V+ + L +++ N Sbjct: 294 SLSAINSDVFGVGRMLHGMAQQGHAPKVFTNTSDRGAP----WVTVVVMMVALLMAVYLN 349 Query: 368 ----QTVYLWLLNTSGMTGFIAWLGIAISHYRFRR 398 + V+L + + + W+ I +S FRR Sbjct: 350 YLMPEKVFLVIASLATFATVWVWIMILLSQIAFRR 384 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: 691 Number of extensions: 43 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: 451 Length adjustment: 33 Effective length of query: 456 Effective length of database: 418 Effective search space: 190608 Effective search space used: 190608 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 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