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_075618505.1 GY23_RS06985 amino acid permease
Query= TCDB::P15993 (457 letters) >NCBI__GCF_001939075.1:WP_075618505.1 Length = 452 Score = 403 bits (1035), Expect = e-117 Identities = 187/443 (42%), Positives = 285/443 (64%), Gaps = 2/443 (0%) Query: 9 EQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLGE 68 ++L RGLKNRH+QLIA+GGAIGTGLFLG+ I AGP I+ Y + G I FLIMR LGE Sbjct: 4 QELSRGLKNRHVQLIAIGGAIGTGLFLGAGKSIHLAGPSILFAYLLTGIICFLIMRALGE 63 Query: 69 MVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPTW 128 +++ SF F Y G+ A F +GW YW ++ +AMA+LTAVG Y QFW PE+P W Sbjct: 64 LLLSNLKYHSFVDFVRDYLGNMAAFITGWTYWFCWISIAMADLTAVGLYTQFWLPEVPQW 123 Query: 129 VSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSG--NGGPQATV 186 + + V++ +NL VK+FGEMEFWFA+IKVIA++A+I+ G +++ G ++ Sbjct: 124 MPGLIALVILLFMNLATVKLFGEMEFWFALIKVIAILALIVIGIFMIVKGFSTDAGASSF 183 Query: 187 SNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRIL 246 +NLW GG P+G G ++ +++F+F G+ELVG+TA E ++PE+ IPKA N + RIL Sbjct: 184 TNLWSHGGMFPNGLNGFILSFQMVVFAFVGIELVGLTAGETEDPERVIPKAINNIPIRIL 243 Query: 247 IFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVYC 306 IFYIG+L V++S+ PW + SPFV +F +G A +N VVLT+A S NS ++ Sbjct: 244 IFYIGALIVIMSIYPWNAINPMESPFVQVFVAVGIAAAAGIVNFVVLTSAASACNSAIFS 303 Query: 307 NSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMALV 366 SRM++ LA+ NAP LA + VP N + S ++ + V++NYL PE F L+ ++ Sbjct: 304 TSRMIYSLAKDKNAPVPLAKLTSGKVPSNALFFSTVIILIAVVLNYLMPEGVFTLITSIS 363 Query: 367 VSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMTPGM 426 + W + ++H+K+R+ + + ++F LYP N++ L+F+A ++V++ + Sbjct: 364 TVCFIFIWGITVISHLKYRKTRPDLAKKSKFKLPLYPFSNYLILVFLAFIIVVLALAEDT 423 Query: 427 AISVYLIPVWLIVLGIGYLFKEK 449 I++++ PVW I+L + Y +EK Sbjct: 424 RIALFITPVWFILLILIYKMREK 446 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: 564 Number of extensions: 27 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: 457 Length of database: 452 Length adjustment: 33 Effective length of query: 424 Effective length of database: 419 Effective search space: 177656 Effective search space used: 177656 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