Align D-serine/D-alanine/glycine transporter (characterized)
to candidate Pf1N1B4_4976 D-serine/D-alanine/glycine transporter
Query= SwissProt::A0A0H2VDI7 (470 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4976 Length = 473 Score = 536 bits (1381), Expect = e-157 Identities = 263/452 (58%), Positives = 337/452 (74%), Gaps = 1/452 (0%) Query: 9 ADDQAPAEQS-LRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFML 67 +D EQ+ L+R L+NRHIQL+A+GGAIGTGLFMGSGK I+L+G SII +YMIIG + Sbjct: 3 SDTHEITEQAVLQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFV 62 Query: 68 FFVMRAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQ 127 +FVMRAMGELLLSNL +KSF+DFA LGP A +F GW+YW W V + D V + + Q Sbjct: 63 YFVMRAMGELLLSNLNFKSFADFAGAYLGPRAAFFLGWSYWLSWSVAVVGDAVVVGGFFQ 122 Query: 128 FWFPGLSDWVASLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHF 187 +WFP + W+ ++ +++ L LN+ TVK+FGE+EFWFA+IKI+A+V+LI V ++++A F Sbjct: 123 YWFPDVPAWIPAIGMMLTLFALNVLTVKLFGEVEFWFAIIKIIAVVALISVSVLLIASSF 182 Query: 188 QSPTGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPR 247 SPTGV AS HL + FP GL GFFAGFQ+A+F+F G EL+GT AAET+ PEK+LP+ Sbjct: 183 VSPTGVTASLTHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRSPEKTLPK 242 Query: 248 AINSIPIRIIMFYVFSLIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSA 307 AINSIP+RII+FYV SL+ I++VT W V P KSPFVELF++ G PAAA ++NFVVLTSA Sbjct: 243 AINSIPLRIILFYVLSLVCIIAVTSWQQVSPNKSPFVELFLIAGFPAAAGIVNFVVLTSA 302 Query: 308 ASSANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPS 367 ASSANSGVFS+SRMLFGLA G AP F +LSK +VP L F+ +L GV++L++ P Sbjct: 303 ASSANSGVFSSSRMLFGLADLGNAPGIFRRLSKNSVPLISLAFTTFLMLLGVLLLFIIPE 362 Query: 368 VIGAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFV 427 V+ AFT+++TVSAIL +F W+ IL SY+ YRK RP LH +S YKMP G M W +AF Sbjct: 363 VMTAFTIVSTVSAILVIFTWSTILASYIAYRKARPDLHAQSRYKMPGGVPMAWFSLAFLA 422 Query: 428 FVLVLLTLEDDTRQALLVTPLWFIALGLGWLF 459 FVL LL L DTR AL V P WFI L + + F Sbjct: 423 FVLCLLALRPDTRLALCVMPAWFIWLAIAYQF 454 Lambda K H 0.329 0.141 0.441 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: 721 Number of extensions: 26 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: 473 Length adjustment: 33 Effective length of query: 437 Effective length of database: 440 Effective search space: 192280 Effective search space used: 192280 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:
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