Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate 14540 b0402 predicted cryptic proline transporter (NCBI)
Query= TCDB::P24207 (458 letters) >FitnessBrowser__Keio:14540 Length = 457 Score = 395 bits (1014), Expect = e-114 Identities = 201/446 (45%), Positives = 288/446 (64%), Gaps = 11/446 (2%) Query: 19 LHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQLGEMV 78 L RGL RHI+ +ALG AIGTGLF G AI+MAGP+VLL Y + GI A++IMR LGEM Sbjct: 7 LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGIAAYIIMRALGEMS 66 Query: 79 VEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVPTWIW 138 V P + SF+ +A + GP AG+++GW Y ++V +A++TA GIYM WFP VP WIW Sbjct: 67 VHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPTVPHWIW 126 Query: 139 AAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMI--GFGLWLLFSGHGGEKASIDN 196 + +II AVNL++V+++GE EFWF+ KV II MI GFG+ + G+GG+ I N Sbjct: 127 VLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMIVAGFGIIIWGIGNGGQPTGIHN 186 Query: 197 LWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVVYRILLF 256 LW GGFF+ GW G+++SL ++MF++GG+E+IGITA EA+DPEKSIP+A+N V RIL+F Sbjct: 187 LWSNGGFFSNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246 Query: 257 YIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGVYSNS 316 Y+G+L V++++YPW +V + SPFV+ F ++ AS LNFV+L ASLS NS V+ Sbjct: 247 YVGTLFVIMSIYPWNQVGTAGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGVG 306 Query: 317 RMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLLMALVVA 376 RML G++ QG+APK ++ SRRG+P ++++ V +NY++P+ F ++ +L Sbjct: 307 RMLHGMAEQGSAPKIFSKTSRRGIPWVTVLVMTTALLFAVYLNYIMPENVFLVIASLATF 366 Query: 377 TLLLNWIMICLAHLRFRAAMRRQGRETQFKALLYPFGNYLCIAFLGMILLLMCT-----M 431 + WIMI L+ + F RR+ + KAL + + G+I LL Sbjct: 367 ATVWVWIMILLSQIAF----RRRLPPEEVKALKFKVPGGVATTIGGLIFLLFIIGLIGYH 422 Query: 432 DDMRLSAILLPVWIVFLFMAFKTLRR 457 D R+S + WIV L + + RR Sbjct: 423 PDTRISLYVGFAWIVVLLIGWMFKRR 448 Lambda K H 0.329 0.143 0.447 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: 654 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: 458 Length of database: 457 Length adjustment: 33 Effective length of query: 425 Effective length of database: 424 Effective search space: 180200 Effective search space used: 180200 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 17 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