Align Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized)
to candidate WP_013076931.1 BTUS_RS15100 amino acid permease
Query= TCDB::P15993 (457 letters) >NCBI__GCF_000092905.1:WP_013076931.1 Length = 462 Score = 421 bits (1082), Expect = e-122 Identities = 208/447 (46%), Positives = 291/447 (65%), Gaps = 7/447 (1%) Query: 10 QLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLGEM 69 +L RGLK RH+QLIALGGAIG GLFLGSA I AGP + + Y + G + FLIMR LGE+ Sbjct: 6 ELVRGLKERHLQLIALGGAIGVGLFLGSARAIHLAGPALTISYLVGGLVIFLIMRALGEL 65 Query: 70 VVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPTWV 129 + +PVAGSFS +A ++ G +AGF +GW YW +++ AMAE+TAVG Y+++W+P +P W+ Sbjct: 66 ALYKPVAGSFSTYAEEFVGPWAGFITGWTYWFMWITTAMAEITAVGVYVRYWFPAVPQWL 125 Query: 130 SAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSG--NGGPQATVS 187 A + VV+ +NL V +GE EFWFA+IKV+ +VAMI+ G ++ G N G S Sbjct: 126 PALIALVVMFLVNLIAVGAYGEFEFWFALIKVVTIVAMIVVGLLIILFGVWNQGVPVGFS 185 Query: 188 NLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRILI 247 NLW GGF P G G ++ + ++MF++ G+EL+G+TA EA +P ++IP ATN++I+RILI Sbjct: 186 NLWSHGGFFPTGIGGALLALQMVMFAYVGVELIGVTAGEARDPSKTIPSATNKIIWRILI 245 Query: 248 FYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVYCN 307 FY+G+L +++SL PW + A SPFVL F +G A+ +N VVLTAALS NS V+ Sbjct: 246 FYVGALVIIMSLYPWNELDAQNSPFVLTFQRIGFPAAADVINFVVLTAALSSCNSGVFST 305 Query: 308 SRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMALVV 367 RML+ LAQ G AP+ L + R VP I SA V + V++NY+ P+ F + +L Sbjct: 306 GRMLYSLAQYGQAPRFLRGLSSRRVPAAAIAASAAVMLVGVILNYVVPQQVFTYVTSLGA 365 Query: 368 SALVINWAMISLAHMKFRR---AKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMTP 424 A + W MI +AHM +RR A Q Q V R P P+ NWI L F+A V+V++L P Sbjct: 366 EAAIWTWGMILVAHMAYRRRVAAGQVQAVKYRMPG--SPVTNWIGLAFLALVVVLLLFDP 423 Query: 425 GMAISVYLIPVWLIVLGIGYLFKEKTA 451 ++ Y+ VW +L I Y F + A Sbjct: 424 DTRVAFYVALVWFAILVIAYQFVRRRA 450 Lambda K H 0.328 0.141 0.434 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: 651 Number of extensions: 45 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: 457 Length of database: 462 Length adjustment: 33 Effective length of query: 424 Effective length of database: 429 Effective search space: 181896 Effective search space used: 181896 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 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