Align Amino acid permease-associated region (characterized, see rationale)
to candidate H281DRAFT_05687 H281DRAFT_05687 amino acid/polyamine/organocation transporter, APC superfamily
Query= uniprot:B2SZ32 (555 letters) >FitnessBrowser__Burk376:H281DRAFT_05687 Length = 531 Score = 1030 bits (2664), Expect = 0.0 Identities = 503/531 (94%), Positives = 522/531 (98%) Query: 25 VKSSIQRNIGPFALMLTGLGSIIGSGWLFGAWKAAKIAGPAAVCAWVIGAVVILAIALTY 84 VKSSIQRNIGPFALMLTGLGSIIGSGWLFGAWKAAKIAGPA++CAW+IGAVVILAIALTY Sbjct: 1 VKSSIQRNIGPFALMLTGLGSIIGSGWLFGAWKAAKIAGPASICAWIIGAVVILAIALTY 60 Query: 85 AELGAMFPESGGMVRYARYSHGALVGFISAWANWIAIVSVIPIEAEASIQYMSTWPYPWA 144 AELGAMFPESGGMVRYARYSHGALVGFISAWANWIAIVSVIPIEAEASIQYMSTWPY WA Sbjct: 61 AELGAMFPESGGMVRYARYSHGALVGFISAWANWIAIVSVIPIEAEASIQYMSTWPYEWA 120 Query: 145 HALFVDGSLTTNGLLLSAALVIIYFMLNYWGVKLFARANSAITIFKFLIPGATILGLMFA 204 HALFVDGSLTTNGLLLSAALVIIYF+LNYWGVKLFARANSAITIFKFLIPGATILGLM Sbjct: 121 HALFVDGSLTTNGLLLSAALVIIYFLLNYWGVKLFARANSAITIFKFLIPGATILGLMLT 180 Query: 205 GFHKENFGEASTFAPYGWSAVLTAVSTSGIVFAFNGFQSPINLAGEARNPAKSVPFAVIG 264 GFHKENFGE STFAPYGWSAVLTAV+TSGIVFAFNGFQSPINLAGEARNPAKSVPFAVIG Sbjct: 181 GFHKENFGETSTFAPYGWSAVLTAVATSGIVFAFNGFQSPINLAGEARNPAKSVPFAVIG 240 Query: 265 SILLALVIYVLLQIAYIGAVNPSDVMKGWSHFNFASPFAELAIALNLNWLAILLYVDAFV 324 SILLALVIYVLLQ+AYIGAV+P+DVMKGWSHFNFASPFAELAIALNLNWLAILLYVDAFV Sbjct: 241 SILLALVIYVLLQVAYIGAVSPADVMKGWSHFNFASPFAELAIALNLNWLAILLYVDAFV 300 Query: 325 SPSGTGTTYMATTSRMIYAMERNNTMPKMFGNVHPFYGVPRQAMWFNLLVSFIFLFFFRG 384 SPSGTGTTYMATT+RMIYAMERNNTMPK+FGNVHPFYGVPR AMWFNLLVSFIFLFFFRG Sbjct: 301 SPSGTGTTYMATTTRMIYAMERNNTMPKIFGNVHPFYGVPRPAMWFNLLVSFIFLFFFRG 360 Query: 385 WSSLAAVISVATVISYLTGPISLMALRRAATDLERPLHIPGMKIIAPFAFVCASLILYWA 444 WSSLAAVISVATVISYLTGPISLMALRRAATDLERPLHIPGM++IAPFAFVCASLILYWA Sbjct: 361 WSSLAAVISVATVISYLTGPISLMALRRAATDLERPLHIPGMQVIAPFAFVCASLILYWA 420 Query: 445 KWPLTGEIILLMVVALPVYFYFQAKSGFAGWGRDLKAAWWLVAYLPVMAILSLIGSKQFG 504 KWPLTGEIILLMVVALPVYFYFQAKSGFAGWGRDLKAAWWLVAYLP+MAILSLIGSK+FG Sbjct: 421 KWPLTGEIILLMVVALPVYFYFQAKSGFAGWGRDLKAAWWLVAYLPIMAILSLIGSKEFG 480 Query: 505 GHDLIPYGWDMVVVIAFSLVFYYWGVTSGYRSEYLDERSEHDEVLEGMGAH 555 GH ++PYGWDM+VVIAFSLVFYYWGV SGYRSEYL+ER HDEVLEG+GAH Sbjct: 481 GHGILPYGWDMLVVIAFSLVFYYWGVHSGYRSEYLEERQTHDEVLEGIGAH 531 Lambda K H 0.326 0.139 0.445 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: 1410 Number of extensions: 49 Number of successful extensions: 1 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: 555 Length of database: 531 Length adjustment: 35 Effective length of query: 520 Effective length of database: 496 Effective search space: 257920 Effective search space used: 257920 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: 52 (24.6 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