Align general amino acid permease AGP1 (characterized)
to candidate WP_008508798.1 BIBO1_RS14845 amino acid permease
Query= CharProtDB::CH_091105 (633 letters) >NCBI__GCF_000182725.1:WP_008508798.1 Length = 467 Score = 179 bits (454), Expect = 2e-49 Identities = 126/402 (31%), Positives = 199/402 (49%), Gaps = 32/402 (7%) Query: 116 LKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCIIQACGEM 175 L + + RH+ +IA+G IGTGL +G+G A+ AGP+ LLI YAI G +L+ +++A GE+ Sbjct: 19 LARNLSNRHLQLIAIGGTIGTGLFMGSGKAVSLAGPSILLI-YAITGFMLFFVMRALGEI 77 Query: 176 ALVYSNLTGGYNAYPSFLVDDGFG----FAVAWVYCLQWLCVCPLELVTASMTIKYWTTS 231 L SNL Y ++ F D G F W Y L W+ E+V S + +W Sbjct: 78 LL--SNLQ--YRSFADF-AGDYLGPCAQFFTGWTYWLCWIVTAVAEVVAVSGYVSFWFPH 132 Query: 232 VNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGA----G 287 + P + + +++ +N+ R + E EF+F KI+ + G I GI + + G G Sbjct: 133 LAPWIPALGLITILLILNLPTVRNFGEIEFWFALIKIITIIGLIITGIYMLMTGFVLPNG 192 Query: 288 NDGFIGGKYWHDPGAF-NGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKAI 346 I W+ G F NG G A + FAF G E + AE NP + + Sbjct: 193 TQASIA-HLWNHGGFFPNGS------LGFIAGFQISVFAFVGIELVGTAAAEAENPMRNL 245 Query: 347 PGAAKQMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASHGVRVVPH 406 P A + RI+ ++ + ++ + P+N +SP+V + G+ + H Sbjct: 246 PKAINNIPIRIVLFYIGALFVIITVTPWNQVD--------PNSSPFVAMFSLAGIGIAAH 297 Query: 407 FINAVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFAV- 465 FIN V+L S S +NS YS++R+ L+ G APK FS + P+ A+ S +F + Sbjct: 298 FINFVVLTSASSSSNSGIYSTSRMVYGLATVGLAPKAFSKLSNRKVPVHALIFSCIFLLS 357 Query: 466 -IAFCAASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRR 506 + A QVFT + IS L +F W+ I +S+L++RR Sbjct: 358 SVVLLYAGQSMIQVFTLVTTISALLFIFIWSIILVSYLQYRR 399 Lambda K H 0.324 0.138 0.424 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: 671 Number of extensions: 32 Number of successful extensions: 6 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: 633 Length of database: 467 Length adjustment: 35 Effective length of query: 598 Effective length of database: 432 Effective search space: 258336 Effective search space used: 258336 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: 41 (22.0 bits) S2: 52 (24.6 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