Align Proline-specific permease (ProY) (characterized)
to candidate WP_084935844.1 HA51_RS17310 proline-specific permease ProY
Query= TCDB::P37460 (456 letters) >NCBI__GCF_002095475.1:WP_084935844.1 Length = 451 Score = 764 bits (1972), Expect = 0.0 Identities = 377/449 (83%), Positives = 407/449 (90%) Query: 1 MESNNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMR 60 M+ NKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGG AYIIMR Sbjct: 1 MQETNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGAIAYIIMR 60 Query: 61 ALGEMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPA 120 ALGEMSV+NP ASSFSRYAQ+ LGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFP Sbjct: 61 ALGEMSVNNPQASSFSRYAQDYLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPE 120 Query: 121 VPHWIWVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQ 180 VPHWIWVLSVVLII INLMSVKVFGE+EFWFSFFKVATIIIMI+AG GII WGIGNGGQ Sbjct: 121 VPHWIWVLSVVLIIGGINLMSVKVFGEVEFWFSFFKVATIIIMILAGFGIIFWGIGNGGQ 180 Query: 181 PTGIHNLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVP 240 PTGIHNLWSNGGFF++G +GM++SLQMVMFAYGGIEIIGITAGEA+DP KSIPRAINSVP Sbjct: 181 PTGIHNLWSNGGFFAHGIVGMLLSLQMVMFAYGGIEIIGITAGEAEDPAKSIPRAINSVP 240 Query: 241 MRILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINS 300 +RILVFYVGTLFVIMSIYPWNQVGT GSPFVLTFQH+GI AAS+LNFVV+TASLSAINS Sbjct: 241 LRILVFYVGTLFVIMSIYPWNQVGTQGSPFVLTFQHLGIAAAASLLNFVVITASLSAINS 300 Query: 301 DVFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVI 360 DVFGVGRMLHGMA+QG APKVF TS RG PWVTV+VM +ALL AVYLNY+MPE VFLVI Sbjct: 301 DVFGVGRMLHGMAQQGHAPKVFTNTSDRGAPWVTVVVMMVALLMAVYLNYLMPEKVFLVI 360 Query: 361 ASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIG 420 ASLATFATVWVWIMILLSQIAFRR++ +E L+F +PGG T G+ FLVFIIALIG Sbjct: 361 ASLATFATVWVWIMILLSQIAFRRKIGAQEAGKLQFALPGGSATAWVGVAFLVFIIALIG 420 Query: 421 YHPDTRISLYVGFAWIVLLLIGWIFKRRR 449 Y PDTR+SLY GFAWI+LLL+ W ++R Sbjct: 421 YFPDTRVSLYAGFAWILLLLLAWPLAKKR 449 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: 831 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: 456 Length of database: 451 Length adjustment: 33 Effective length of query: 423 Effective length of database: 418 Effective search space: 176814 Effective search space used: 176814 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