Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate PP_1299 PP_1299 putative amino acid ABC transporter - membrane subunit
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__Putida:PP_1299 Length = 365 Score = 397 bits (1019), Expect = e-115 Identities = 204/367 (55%), Positives = 251/367 (68%), Gaps = 13/367 (3%) Query: 18 PAPSLESGAVSWLRKNLFATPKDTALTIISLLILAWLVPPAIQWLFIDAAWSGGGRGVCA 77 P P G ++W+R NLF++ +T LT+ ++ ++ +VPP +QW IDA W G R C Sbjct: 11 PPPVKTVGVLAWMRANLFSSWLNTLLTLFAIYLVWLIVPPLLQWALIDANWVGTTRADCT 70 Query: 78 TLSQGGSQPEGWSGACWAFVNAKFAQFLFGRYPLDERWRPALVGILFVLLLVPMLIPRIP 137 GACW FV +F QF++G YP + RWR L L VL P+ I R P Sbjct: 71 K-----------EGACWVFVQQRFGQFMYGYYPTELRWRVDLTVWLAVLGAAPLFIKRFP 119 Query: 138 YKGLNALLLLVALPILSAILLPGGWFGLTYVETPLWGGLMVTLVLSFVGIAVSLPLGILL 197 K L LV P+L+ LL GG+ GL V T WGGLM+TLV++ VGI +LPLGILL Sbjct: 120 RKAFYGLGFLVLYPVLAYTLLHGGYLGLESVPTSQWGGLMLTLVIATVGIVGALPLGILL 179 Query: 198 ALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLFLPQGVTFDKFLRALIGVSL 257 ALGRRS MP +K++C FIE RGVPLITVLFM+SVMLPLFLP+G++FDK LRA+IGV L Sbjct: 180 ALGRRSRMPAVKVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMSFDKLLRAMIGVIL 239 Query: 258 FASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVIPGIVNTFIGLF 317 F SAY+AEVVRGGLQAIPKGQYE A ++GL +W+ MG ++LPQALKLVIPGIVNTFI LF Sbjct: 240 FQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALF 299 Query: 318 KDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTGLIFAGFVFWLFCFGMSRYSGFMER 377 KDTSLV IIG+FDLL V+ +D W T G +FA VFW+FCFGMSRYS +ER Sbjct: 300 KDTSLVIIIGLFDLLNSVKQAAADPAWLGMAT--EGYVFAALVFWIFCFGMSRYSMHLER 357 Query: 378 LLDRSQR 384 LD + Sbjct: 358 KLDTGHK 364 Lambda K H 0.329 0.144 0.454 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: 571 Number of extensions: 24 Number of successful extensions: 3 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: 384 Length of database: 365 Length adjustment: 30 Effective length of query: 354 Effective length of database: 335 Effective search space: 118590 Effective search space used: 118590 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 (21.8 bits) S2: 50 (23.9 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