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_084934657.1 HA51_RS11575 D-serine/D-alanine/glycine transporter
Query= TCDB::P15993 (457 letters) >NCBI__GCF_002095475.1:WP_084934657.1 Length = 463 Score = 349 bits (896), Expect = e-101 Identities = 179/456 (39%), Positives = 275/456 (60%), Gaps = 6/456 (1%) Query: 1 MMEGQQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAF 60 ++E +Q E+L+R L NRHIQLIA+GGAIGTGLF+GS I AGP II Y I GF+ F Sbjct: 9 LIEAEQP-EKLRRNLHNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLF 67 Query: 61 LIMRQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQF 120 +MR +GE+++ SFS FA G +AG+ +GW YW +V+ +A++ A+ Y Q Sbjct: 68 FVMRAMGELLLSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGIADVVAISAYFQL 127 Query: 121 WYPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLL---FS 177 W+P W+SA + A+N+ VK+FGEMEFWFAIIK++A+VA+II G L+ + Sbjct: 128 WFPGFSIWMSALLCIFAFLALNIATVKLFGEMEFWFAIIKIVAIVALIITGIVLVSMHYP 187 Query: 178 GNGGPQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKA 237 G A++SN+WD GG P G +G I +F+F G+ELVG AAE +P + +P+A Sbjct: 188 SPNGTTASLSNIWDHGGMFPKGLSGFFAGFQIAVFAFVGIELVGTAAAETKDPHKVLPRA 247 Query: 238 TNQVIYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAAL 297 N + RI++FY+ +L V++++ PW +V + SPFV +F +G A+ +N VVLT+A Sbjct: 248 INAIPVRIIMFYVLALLVIMAVTPWNQVLPNRSPFVEMFVLIGLPAAASIVNFVVLTSAA 307 Query: 298 SVYNSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPES 357 S NS ++ SRMLFGLA+ G A KA + R VP + S L + V + YL P+ Sbjct: 308 SSANSGIFSTSRMLFGLAELGVAHKAFGRLSARAVPTTGLFFSCLCLLVGVALIYLIPDV 367 Query: 358 AFGLLMALVVSALVIN--WAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAA 415 M VSA++ W +I +++ +R+ ++ ++F L W+C+ F A Sbjct: 368 MTVFTMVTTVSAILFMFVWTIILCSYLAYRKQHPQRHAASKFKMPLGKFMCWVCMAFFAF 427 Query: 416 VLVIMLMTPGMAISVYLIPVWLIVLGIGYLFKEKTA 451 VLV++ + ++ + P+W ++L +G+L + + A Sbjct: 428 VLVLLTLQEDTRQALMVTPLWFVILTLGWLLRRRKA 463 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: 612 Number of extensions: 35 Number of successful extensions: 4 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: 463 Length adjustment: 33 Effective length of query: 424 Effective length of database: 430 Effective search space: 182320 Effective search space used: 182320 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