Align Proline-specific permease (ProY) (characterized)
to candidate WP_008347408.1 BA79_RS16380 amino acid permease
Query= TCDB::P37460 (456 letters) >NCBI__GCF_000691145.1:WP_008347408.1 Length = 448 Score = 373 bits (958), Expect = e-108 Identities = 180/447 (40%), Positives = 283/447 (63%), Gaps = 2/447 (0%) Query: 3 SNNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRAL 62 + +LKR LS RH++ +A+G IGTGLF GS AI++AGPS++ AY+I G+A + +MRAL Sbjct: 2 AQQELKRDLSNRHVQLIAIGGTIGTGLFLGSGKAIQLAGPSIIFAYLIVGMAIFFVMRAL 61 Query: 63 GEMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVP 122 GE+ + S + A++ LGP A ++TGWTY F ++ A+ADV A G+Y+ WF +P Sbjct: 62 GELLLSKAGYQSLTDIAEDYLGPWASFVTGWTYWFCWIMTAMADVIAVGVYVQYWFD-IP 120 Query: 123 HWIWVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPT 182 WI + +LI+ NL++VK+FGE+EFWF+ KV TI+++I GI +++ G P Sbjct: 121 QWIPAIICLLILLGFNLLTVKLFGEMEFWFALIKVITILLLIGVGIVLLIIGFQTDAGPV 180 Query: 183 GIHNLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMR 242 + NLWS+GG F NG G ++S QMV+FAY G+E++G++A E +P+K+IP AIN +P+R Sbjct: 181 TVTNLWSHGGLFPNGVTGFLLSFQMVIFAYVGVELVGVSAAETANPQKNIPSAINKIPLR 240 Query: 243 ILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDV 302 IL FYVG +FV++ I PW ++ + SPFV TF +GI AA ++NFVVLT++ SA NS + Sbjct: 241 ILFFYVGAIFVLLCINPWTELSASESPFVKTFGLIGIPVAAGLINFVVLTSAASACNSGM 300 Query: 303 FGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVIAS 362 F R+L+ ++ Q P F + ++ +P + V TI + L+ ++PE F ++ + Sbjct: 301 FSTSRILYNLSHQKQGPASFGRLNKHAVPSNALFVSTIVVSVGALLSKLIPEQAFGIVTT 360 Query: 363 LATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIGYH 422 ++ +WVW +IL+ + + ++ PE KA FK P IA L+ I+ ++ + Sbjct: 361 ISAICFIWVWSIILICHLKY-KKTRPELHKASTFKAPFTPFVNIAVLVLFAAILVIMLFA 419 Query: 423 PDTRISLYVGFAWIVLLLIGWIFKRRR 449 TR +L + W L + + K+RR Sbjct: 420 DATRPALLLTPVWFGFLFLIYARKKRR 446 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: 614 Number of extensions: 34 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: 456 Length of database: 448 Length adjustment: 33 Effective length of query: 423 Effective length of database: 415 Effective search space: 175545 Effective search space used: 175545 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