Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate SMc02120 SMc02120 general L-amino acid transport permease ABC transporter protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >FitnessBrowser__Smeli:SMc02120 Length = 384 Score = 400 bits (1027), Expect = e-116 Identities = 204/367 (55%), Positives = 251/367 (68%), Gaps = 13/367 (3%) Query: 11 PPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTTRADCT 70 P P G V+W+R N+F++ +T LT+ + ++ +VPP +QW +DA W G R C Sbjct: 18 PAPSLESGAVSWLRKNLFATPKDTALTIISLLILAWLVPPAIQWLFIDAAWSGGGRGVCA 77 Query: 71 K-----------EGACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLFISRFP 119 GACW F+ +F QF++G YP D RWR L L V+ + P+ I R P Sbjct: 78 TLSQGGSQPEGWSGACWAFVNAKFAQFLFGRYPLDERWRPALVGILFVLLLVPMLIPRIP 137 Query: 120 RKAIYGLSFLVLYPISAWCLLHGGVFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVL 179 K + L LV PI + LL GG FGL V T WGGLM+TLV++ VGI +LPLGI+L Sbjct: 138 YKGLNALLLLVALPILSAILLPGGWFGLTYVETPLWGGLMVTLVLSFVGIAVSLPLGILL 197 Query: 180 ALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVIL 239 ALGRRSNMP I+++C FIE RGVPLITVLFM+SVMLPLFLP+G+ FDK LRALIGV L Sbjct: 198 ALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLFLPQGVTFDKFLRALIGVSL 257 Query: 240 FQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALF 299 F SAY+AEVVRGGLQAIPKGQYE A ++GL +W+ MG ++LPQALKLVIPGIVNTFI LF Sbjct: 258 FASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVIPGIVNTFIGLF 317 Query: 300 KDTSLVIIIGLFDLLNSVKQAAADPKWLGMAT--EGYVFAALVFWIFCFGMSRYSMHLER 357 KDTSLV IIG+FDLL V+ +D W T G +FA VFW+FCFGMSRYS +ER Sbjct: 318 KDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTGLIFAGFVFWLFCFGMSRYSGFMER 377 Query: 358 KLDTGHK 364 LD + Sbjct: 378 LLDRSQR 384 Lambda K H 0.330 0.144 0.469 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: 631 Number of extensions: 28 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: 365 Length of database: 384 Length adjustment: 30 Effective length of query: 335 Effective length of database: 354 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 (21.9 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