Align Amino acid:proton symporter (characterized, see rationale)
to candidate BWI76_RS08460 BWI76_RS08460 dicarboxylate/amino acid:cation symporter
Query= uniprot:A0A0N9WTL5 (431 letters) >FitnessBrowser__Koxy:BWI76_RS08460 Length = 435 Score = 393 bits (1009), Expect = e-114 Identities = 215/433 (49%), Positives = 297/433 (68%), Gaps = 8/433 (1%) Query: 1 MKKNKLPRRIAMGIALGVLVGWACHHFAGSEQSAKEIASYFSMVTDIFLRMIKMIIAPLV 60 MKK L + I +G+ LG++ G ++ A ++ +AK A S+ T IFLRM+KMIIAPLV Sbjct: 1 MKKISLTKMIILGLILGMIAGVIINNMASAD-TAKSYAQDISIFTTIFLRMVKMIIAPLV 59 Query: 61 FATLVGGIASMGNSRSVGRIGARAMAWFVTASVVSLLIGMGLVNLFQPGAGLNMDVAQHA 120 +TLV GIA MG+++++GRI ++ F+ AS++S+ +G+ +VNLFQPGAG+N V A Sbjct: 60 ISTLVVGIAKMGDAKTLGRIFSKTFFLFICASLLSIALGLVIVNLFQPGAGINF-VPHDA 118 Query: 121 TAAVPVNTGDFSLKAFIGHVFPRSIAEAMANNEILQIVVFSLFFGFALA--GVKRAGYTR 178 A V + F+LK FI H P SI +AMA NEILQIVVFS+F G +LA G K + Sbjct: 119 GAVAAVQSEPFTLKVFISHAVPTSIVDAMARNEILQIVVFSIFLGCSLAAIGEKAEPIVK 178 Query: 179 ITDSIEELAKVMFKITDYVMAFAPIGVFAAIASAITTQGLGLLVDYGKLIAEFYLGILIL 238 + DS L VM K+T YVM FAP+ VFAAI+ I +GLG++V G + EFYL + +L Sbjct: 179 VLDS---LVHVMLKLTGYVMLFAPLTVFAAISGLIAERGLGVMVSAGIFMGEFYLTLGML 235 Query: 239 WALLFGAGYLFLGRSVFHLGKLIREPILLAFSTASSESAYPKTIEALEKFGAPKRVSSFV 298 WA+L G + +G + L K I EP LLAF+T+SSE+A+P T++ LEKFG +++SFV Sbjct: 236 WAILIGLSTVIVGPCISRLTKAIFEPALLAFTTSSSEAAFPGTLDKLEKFGVSSKIASFV 295 Query: 299 LPLGYSFNLDGSMMYQAFAILFIAQAYNIDLSFTQQLLILLTLMITSKGMAGVARASVVV 358 LP+GYSFNL GSM Y +FA +FIAQA N+ LS +Q+ +LL LM+TSKGMAGV RAS+VV Sbjct: 296 LPIGYSFNLVGSMAYCSFATVFIAQACNVHLSMGEQITMLLILMLTSKGMAGVPRASMVV 355 Query: 359 VAATLPMFNLPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSESHEEADEEEGEH 418 +AATL FN+PEAGL+L++G+D FLDM R+ATNV+ N++ A+V + E + G Sbjct: 356 IAATLNQFNIPEAGLILLMGVDPFLDMGRSATNVMSNAMGAAIVGRWEGEHYGEGCRGT- 414 Query: 419 APARSRSEPVPVA 431 AP + + P + Sbjct: 415 APVKKPEQDRPAS 427 Lambda K H 0.325 0.138 0.392 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: 460 Number of extensions: 20 Number of successful extensions: 5 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: 431 Length of database: 435 Length adjustment: 32 Effective length of query: 399 Effective length of database: 403 Effective search space: 160797 Effective search space used: 160797 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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