Align Proline-specific permease (ProY) (characterized)
to candidate WP_034525974.1 LOSG293_RS01045 amino acid permease
Query= TCDB::P37460 (456 letters) >NCBI__GCF_000740055.1:WP_034525974.1 Length = 469 Score = 404 bits (1037), Expect = e-117 Identities = 198/446 (44%), Positives = 298/446 (66%), Gaps = 7/446 (1%) Query: 7 LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGEMS 66 ++R LS R ++ +ALG IG GLF GS IK GPSVL+AY I G+ Y IMRALGEM Sbjct: 1 MQRKLSARQMQMIALGGTIGVGLFMGSTSTIKWTGPSVLIAYGIAGIFLYFIMRALGEML 60 Query: 67 VHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPHWIW 126 +P SFS++A E + P+ GY+T W+ F+ ++V ++++ A G YM W+P +P WI Sbjct: 61 YVDPDTGSFSKFATEYMHPVFGYLTAWSNIFQFIVVGMSEMIAIGGYMEFWWPGLPDWIP 120 Query: 127 VLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTGIHN 186 L +L + NL+SVK+FGELEFWFS KV TII+MIVAG+G+I++GIGN P GI N Sbjct: 121 GLIAILFLSLANLISVKMFGELEFWFSLIKVVTIILMIVAGLGLIIFGIGNHMHPIGISN 180 Query: 187 LWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246 +W+NGGFF+ G G I +L +V+ +Y GIE+IG+TAGEA++P ++ +AI S RIL+F Sbjct: 181 MWTNGGFFTGGVKGFIFALSIVLASYQGIELIGVTAGEAENPRHTLVKAIQSTVARILIF 240 Query: 247 YVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGVG 306 Y+G +FVI+SIYPWN++ GSPFV TF +GIT AASI+NFVV+TA+LS NS ++ Sbjct: 241 YIGAIFVIVSIYPWNKLDALGSPFVETFAKIGITAAASIINFVVVTAALSGSNSGIYSAS 300 Query: 307 RMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMP------ENVFLVI 360 RM +A +G PK F K +R G+P+ +V+ +++ + V LN+++P N+F+++ Sbjct: 301 RMAFTLANRGELPKGFLKLNRHGVPYWSVIAISLGIFLGVVLNFLIPIFWPDASNIFVLV 360 Query: 361 ASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIG 420 S + + W +IL+S+I F R++ +++ FK+P V+ + FLV + + Sbjct: 361 YSSSVLPGMIPWFVILISEIRF-RKVHQDKMGDHPFKMPFAPVSNYITIFFLVLTLLFMF 419 Query: 421 YHPDTRISLYVGFAWIVLLLIGWIFK 446 +P+TR+S+ VG ++ ++ I + K Sbjct: 420 VNPETRVSIIVGVIFLAIMTILYFVK 445 Lambda K H 0.329 0.143 0.449 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: 587 Number of extensions: 36 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: 456 Length of database: 469 Length adjustment: 33 Effective length of query: 423 Effective length of database: 436 Effective search space: 184428 Effective search space used: 184428 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 (21.8 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