Align D-serine/D-alanine/glycine transporter (characterized)
to candidate AO356_29455 AO356_29455 amino acid transporter
Query= SwissProt::P0AAE0 (470 letters) >lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29455 AO356_29455 amino acid transporter Length = 484 Score = 532 bits (1371), Expect = e-156 Identities = 257/442 (58%), Positives = 336/442 (76%) Query: 16 EQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMG 75 + +L+R L+NRHIQL+A+GGAIGTGLFMGSGK I+L+G SII +YMIIG ++FVMRAMG Sbjct: 11 QPALQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFVYFVMRAMG 70 Query: 76 ELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSD 135 E+LLSNL +K+F+DFA LGP A +F GW+YW W V + D V + + Q+WFPD+ Sbjct: 71 EMLLSNLNFKTFADFAGAYLGPRAAFFLGWSYWLSWSVAVIGDAVVVGGFFQYWFPDVPA 130 Query: 136 WVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEA 195 W+ ++ +++ L LN+ TV++FGE+EFWFA+IKI+A+V+LI V LV++A F SP+GV A Sbjct: 131 WIPAIGMLMTLFALNVLTVRLFGEIEFWFAIIKIIAVVTLIGVSLVLIASSFVSPSGVTA 190 Query: 196 SFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIR 255 S HL + FP GL GFFAGFQ+A+F+F G EL+GT AAET++PEK+LP+AINSIP+R Sbjct: 191 SLNHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRNPEKTLPKAINSIPLR 250 Query: 256 IIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGV 315 II+FYV AL I++VT W V P KSPFVELF++ G PAAA ++NFVVLTSAASSANSGV Sbjct: 251 IILFYVLALACIIAVTSWQQVSPSKSPFVELFLVAGFPAAAGIVNFVVLTSAASSANSGV 310 Query: 316 FSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMI 375 FS+SRMLFGLA + AP F +LS +VP L F+ + +L GV++L++ P V+ AFT++ Sbjct: 311 FSSSRMLFGLANQDNAPGIFRRLSGNSVPLLSLAFTTLLMLVGVLLLFIVPEVMTAFTIV 370 Query: 376 TTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVVVLLTL 435 +TVSAIL +F W+ IL SY+ YRK+RP LH KS YKMP G M W +AF FV+ LL L Sbjct: 371 STVSAILVIFTWSTILASYIAYRKKRPELHAKSAYKMPGGVPMAWFSLAFLGFVLCLLAL 430 Query: 436 EDDTRQALLVTPLWFIALGLGW 457 DTR ALLV P WFI L + + Sbjct: 431 RPDTRIALLVMPGWFIWLAIAY 452 Lambda K H 0.329 0.141 0.440 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: 733 Number of extensions: 33 Number of successful extensions: 1 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: 470 Length of database: 484 Length adjustment: 33 Effective length of query: 437 Effective length of database: 451 Effective search space: 197087 Effective search space used: 197087 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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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