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_005816838.1 DHAF_RS12190 amino acid permease
Query= TCDB::P15993 (457 letters) >NCBI__GCF_000021925.1:WP_005816838.1 Length = 462 Score = 506 bits (1302), Expect = e-148 Identities = 248/460 (53%), Positives = 323/460 (70%), Gaps = 3/460 (0%) Query: 1 MMEGQQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAF 60 M + H +L RGLKNRHIQ+IALGGAIGTGLF GSA+ IQ GP II+ Y + G F Sbjct: 1 MSSEKDHHVELHRGLKNRHIQMIALGGAIGTGLFYGSATTIQLVGPAIIVSYLLGGTAIF 60 Query: 61 LIMRQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQF 120 I+R LGEM V++PVAG+FS+FAYKY G F GF SGWNYW Y+ V+MAELT VG YI F Sbjct: 61 FIVRALGEMCVDQPVAGAFSYFAYKYLGDFPGFFSGWNYWFNYIAVSMAELTVVGVYINF 120 Query: 121 WYPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNG 180 WYP +P WV+A F V+I INL NV+ FGE EFWFA+IKV+A++AMI FG ++F G G Sbjct: 121 WYPNVPQWVTALAFLVIITLINLINVEAFGEFEFWFALIKVVAILAMIAFGLVMIFFGLG 180 Query: 181 GPQAT-VSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATN 239 A SNLW GGFLP+G GL++ + I+MFSFGG+EL+GITAAEAD+P++SIPKA N Sbjct: 181 EQGAVGFSNLWTHGGFLPNGVWGLLLSLVIVMFSFGGVELIGITAAEADDPKRSIPKAIN 240 Query: 240 QVIYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSV 299 QV++RILIFYIG+L +L+ L PW ++ SPFV IF +G A+ LN VVLTAALSV Sbjct: 241 QVVWRILIFYIGALTILMILYPWDQIGTSGSPFVEIFSAIGIPAAAHILNFVVLTAALSV 300 Query: 300 YNSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAF 359 YNS +Y N RML GLA QGNAPK L V + G+P+N + S+ VT + V++N+L P F Sbjct: 301 YNSGIYSNGRMLHGLALQGNAPKFLTKVSRNGIPINGVFASSAVTLIAVILNFLVPGKVF 360 Query: 360 GLLMALVVSALVINWAMISLAHMKFRRAKQEQG--VVTRFPALLYPLGNWICLLFMAAVL 417 L+++ A + NWAMI + ++FR+ + E+G +F LYP+ N+I L F+A V+ Sbjct: 361 LYLISIATIAGIFNWAMILVTQLRFRKVEAEKGREDQLQFKMPLYPISNYIALAFLAMVV 420 Query: 418 VIMLMTPGMAISVYLIPVWLIVLGIGYLFKEKTAKAVKAH 457 V+M P M S+Y+ P+W+I+L IGY F + + H Sbjct: 421 VLMAYIPDMVYSLYIGPIWIIILYIGYKFLRRNPETKPPH 460 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: 649 Number of extensions: 32 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