Align Proline-specific permease (ProY) (characterized)
to candidate 14258 b0112 aromatic amino acid transporter (NCBI)
Query= TCDB::P37460 (456 letters) >FitnessBrowser__Keio:14258 Length = 457 Score = 389 bits (1000), Expect = e-113 Identities = 196/451 (43%), Positives = 290/451 (64%), Gaps = 11/451 (2%) Query: 2 ESNNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRA 61 + +LKRGL RHI+ +ALG AIGTGLF GSA I+ AGP ++L Y I G A++IMR Sbjct: 6 QHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQ 65 Query: 62 LGEMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAV 121 LGEM V P A SFS +A + G AG+ +GW Y ++VA+A++TA G Y+ W+P + Sbjct: 66 LGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEI 125 Query: 122 PHWIWVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQP 181 P W+ ++I AINL +VKVFGE+EFWF+ KV ++ MI+ G G +++ GNGG Sbjct: 126 PTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFG-GWLLFS-GNGGPQ 183 Query: 182 TGIHNLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPM 241 + NLW GGF +G+ G++M + ++MF++GG+E++GITA EA +PE+SIP+A N V Sbjct: 184 ATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIY 243 Query: 242 RILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSD 301 RIL+FY+G+L V++S+ PW +V + SPFVL F +G TF A+ LN VVLTA+LS NS Sbjct: 244 RILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSC 303 Query: 302 VFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVIA 361 V+ RML G+A+QG+APK A +RG+P T+LV + V +NY+ PE+ F ++ Sbjct: 304 VYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLM 363 Query: 362 SLATFATVWVWIMILLSQIAFRRRLPPEEV----KALKFKVPGGVVTTIAGLIFLVFIIA 417 +L A V W MI L+ + FRR + V AL + + + L+F+ ++ Sbjct: 364 ALVVSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWIC-----LLFMAAVLV 418 Query: 418 LIGYHPDTRISLYVGFAWIVLLLIGWIFKRR 448 ++ P IS+Y+ W+++L IG++FK + Sbjct: 419 IMLMTPGMAISVYLIPVWLIVLGIGYLFKEK 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: 609 Number of extensions: 39 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: 457 Length adjustment: 33 Effective length of query: 423 Effective length of database: 424 Effective search space: 179352 Effective search space used: 179352 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