Align Valine amino-acid permease; Branched-chain amino-acid permease 3 (characterized)
to candidate WP_003943879.1 C1M55_RS01060 amino acid permease
Query= SwissProt::P41815 (604 letters) >NCBI__GCF_002893965.1:WP_003943879.1 Length = 469 Score = 185 bits (469), Expect = 4e-51 Identities = 122/404 (30%), Positives = 209/404 (51%), Gaps = 20/404 (4%) Query: 86 LKKSMKSRHVVMMSLGTGIGTGLLVANAKGLSLAGPGSLVIGYVMVSFVTYFMVQAAGEM 145 L+ ++K RH+ M+++ IG GL V + + GPG L I Y + V +++ GEM Sbjct: 9 LQHTLKKRHLSMIAIAGVIGAGLFVGSGVAIQETGPGVL-ISYALAGVVVILVMRMLGEM 67 Query: 146 GVTYPTLPGNFNAYNSIFISKSFGFATTWLFCIQWLTVLPLELITSSMTVKYWNDTINAD 205 P G+F++Y I + GF+ WL+ W+ VL +E ++ + W + Sbjct: 68 SAASPET-GSFSSYADKAIGRWAGFSIGWLYAWFWIIVLGIEATAGALIMNRWVPGVPQW 126 Query: 206 VFIVIFYVFLLFIHFFGVKAYGETEFIFNSCKILMVAGFIILSVVINCGGA-GVDGYIGG 264 + +I + L + VK++GE EF F S K++ + F+ + +V CG GV+ Sbjct: 127 TWALILMIVLTLTNIISVKSFGEFEFWFASIKVVAIIAFLGMGIVAICGWMPGVEAPGMT 186 Query: 265 KYWRDPGSFAEGSGATRFKGICYILVSAYFSFGGIELFVLSINEQSNPRKSTPVAAKRSV 324 G G+GA + +LV FSF G E+ ++ E +NP ++ A K V Sbjct: 187 NLTGHGGFLPNGTGAM----LAAVLV-VVFSFFGAEIATIAAGESANPLEAVRAAVKSVV 241 Query: 325 YRILIIYLLTMILIGFNVPHNNDQLMGSGGSATHASPYVLAASIHKVRVIPHIINAVILI 384 +RILI Y+ ++ ++ +P ++ ++ SPYV + + +I++ V+L Sbjct: 242 WRILIFYIGSIAVVVTLLPWDS--------ASVALSPYVAVMDSYGIPAAGNIMDVVVLT 293 Query: 385 SVISVANSALYAAPRLMCSLAQQGYAPKFLNYIDREGRPLRALVVCSLVG--VVGFVACS 442 SV+S NS LY A R++ SLA +G APK L+ I++ G P+RA++V ++VG VG S Sbjct: 294 SVLSCLNSGLYTASRMIFSLAGRGDAPKSLSRIEKTGVPMRAVLVSTIVGFLTVGMNYLS 353 Query: 443 PQEEQAFTWLAAIAGLSELFTWSGIMLSHIRFRKAMKVQGRSLD 486 P ++ F +L +G LF W I +S +R R+ ++ G+ L+ Sbjct: 354 P--DKVFLFLVNSSGAIALFVWLVISVSQLRTRRKLEASGQELE 395 Lambda K H 0.324 0.138 0.420 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: 583 Number of extensions: 34 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: 604 Length of database: 469 Length adjustment: 35 Effective length of query: 569 Effective length of database: 434 Effective search space: 246946 Effective search space used: 246946 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: 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