Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate 14540 b0402 predicted cryptic proline transporter (NCBI)
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Keio:14540 Length = 457 Score = 381 bits (978), Expect = e-110 Identities = 192/442 (43%), Positives = 283/442 (64%), Gaps = 3/442 (0%) Query: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 69 LKRGL RHI+ +ALG AIGTGLF GSA ++ AGPS++L Y IGG+ A++IMR LGEM Sbjct: 7 LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGIAAYIIMRALGEMS 66 Query: 70 AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 129 P A SFS +A + G G+++GW Y ++V++A++TA G Y+ W+P VP W+ Sbjct: 67 VHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPTVPHWIW 126 Query: 130 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLV--SGHGGPQASISN 187 L I A+NL +VK +GE EFWF+ KV +I MI+ G +++ G+GG I N Sbjct: 127 VLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMIVAGFGIIIWGIGNGGQPTGIHN 186 Query: 188 LWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIF 247 LWS+GGFF +G+ G+ L ++MF++GG+E+IGITA EA +P+KSIP+A+N V RIL+F Sbjct: 187 LWSNGGFFSNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246 Query: 248 YICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYANS 307 Y+ +L V++S+YPWN+V GSPFV+ F +G T A++LN VVLTA+LS NS V+ Sbjct: 247 YVGTLFVIMSIYPWNQVGTAGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGVG 306 Query: 308 RMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMALVVA 367 RML+G+AEQG+AP+ K RRG+P++ + + A V +NY++P ++ +L Sbjct: 307 RMLHGMAEQGSAPKIFSKTSRRGIPWVTVLVMTTALLFAVYLNYIMPENVFLVIASLATF 366 Query: 368 ALVLNWALISLTHLKSRRAMVAAG-ETLVFKSFWFPVSNWICLAFMALILVILAMTPGLS 426 A V W +I L+ + RR + + L FK + L F+ I+ ++ P Sbjct: 367 ATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVATTIGGLIFLLFIIGLIGYHPDTR 426 Query: 427 VSVLLVPLWLVVMWAGYAFKRR 448 +S+ + W+VV+ G+ FKRR Sbjct: 427 ISLYVGFAWIVVLLIGWMFKRR 448 Lambda K H 0.327 0.140 0.440 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: 518 Number of extensions: 21 Number of successful extensions: 2 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: 461 Length of database: 457 Length adjustment: 33 Effective length of query: 428 Effective length of database: 424 Effective search space: 181472 Effective search space used: 181472 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 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