Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate SMc02120 SMc02120 general L-amino acid transport permease ABC transporter protein
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__Smeli:SMc02120 Length = 384 Score = 300 bits (768), Expect = 5e-86 Identities = 181/437 (41%), Positives = 242/437 (55%), Gaps = 60/437 (13%) Query: 2 SDTSFVRTEMLAPRPAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQAAAPWL- 60 + SFVR M+ PAP + GA+ W+R+NLF+ P +TALT+ LL WLV A WL Sbjct: 4 NQASFVRASMIEASPAPSLESGAVSWLRKNLFATPKDTALTIISLLILAWLVPPAIQWLF 63 Query: 61 LHGVWNANSLTECRAIIAERWGPEA-TGACWAVIRVRWNQFLFGFYPVDQYWRLFVTFAG 119 + W+ C + PE +GACWA + ++ QFLFG YP+D+ Sbjct: 64 IDAAWSGGGRGVCATLSQGGSQPEGWSGACWAFVNAKFAQFLFGRYPLDER--------- 114 Query: 120 LFLALAPVLFDALPRKLIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFTALAPK 179 W P A++G+LF L Sbjct: 115 -------------------------------------WRP-------ALVGILFVLLLVP 130 Query: 180 LGVPVSAGIGLVVAALFWLYAAAPIEAALQSALPLALPEVDSDQFGGFLLALVIGVTAIV 239 + +P GL AL L A + A L L V++ +GG ++ LV+ I Sbjct: 131 MLIPRIPYKGL--NALLLLVALPILSAILLPGGWFGLTYVETPLWGGLMVTLVLSFVGIA 188 Query: 240 VSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGTNFDLI 299 VSLPLGILLALGR+S+M ++K L IE +RGVPLIT+LF AS++L FLP G FD Sbjct: 189 VSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLFLPQGVTFDKF 248 Query: 300 LRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPG 359 LR +I V+LFA+AY+AEV+RGGL A+P+GQYE AD+LGL +WQ I++PQALK+ IPG Sbjct: 249 LRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVIPG 308 Query: 360 IVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKG--TYWEPYIFVALIFFLFNFS 417 IV++FIGLFKDT+LV+ +G+FD L GI + SD W T IF +F+LF F Sbjct: 309 IVNTFIGLFKDTSLVSIIGMFD-LLGIVRLNFSDTNWATAVTPLTGLIFAGFVFWLFCFG 367 Query: 418 MSRYSMYLERKLKRDHR 434 MSRYS ++ER L R R Sbjct: 368 MSRYSGFMERLLDRSQR 384 Lambda K H 0.329 0.143 0.457 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: 604 Number of extensions: 30 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 434 Length of database: 384 Length adjustment: 31 Effective length of query: 403 Effective length of database: 353 Effective search space: 142259 Effective search space used: 142259 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