Align D-serine/D-alanine/glycine transporter (characterized)
to candidate GFF2849 PS417_14545 amino acid transporter
Query= SwissProt::A0A0H2VDI7 (470 letters) >FitnessBrowser__WCS417:GFF2849 Length = 465 Score = 534 bits (1375), Expect = e-156 Identities = 261/442 (59%), Positives = 335/442 (75%) Query: 18 SLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGEL 77 +L+R L+NRHIQL+A+GGAIGTGLFMGSGK I+L+G SII +YMIIG ++FVMRAMGEL Sbjct: 13 ALQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFVYFVMRAMGEL 72 Query: 78 LLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPGLSDWV 137 LLSNL +KSF+DFA LGP A +F GW+YW W V + D V + + Q+WFP + W+ Sbjct: 73 LLSNLNFKSFADFAGAYLGPRAAFFLGWSYWLSWSVAVIGDAVVVGGFFQYWFPHVPAWM 132 Query: 138 ASLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEASF 197 ++ +++ L LN+ TV++FGE+EFWFA+IK++A+++LI V V++A F SPTGV ASF Sbjct: 133 PAVGMLLTLFALNVLTVRLFGEVEFWFAIIKLIAVLTLIGVSGVLIASSFVSPTGVTASF 192 Query: 198 AHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIRII 257 HL + FP GL GFFAGFQ+A+F+F G EL+GT AAET+ PEK+LP+AINSIP+RII Sbjct: 193 THLLDPQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRAPEKTLPKAINSIPLRII 252 Query: 258 MFYVFSLIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGVFS 317 +FYV +L I++VT W V P KSPFVELF++ G PAAA ++NFVVLTSAASSANSGVFS Sbjct: 253 LFYVLALACIIAVTSWQHVSPSKSPFVELFLVAGFPAAAGIVNFVVLTSAASSANSGVFS 312 Query: 318 TSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMITT 377 SRMLFGLA G AP F +LSK +VP L F+ + +L G+V+L+V P V+ AFT+++T Sbjct: 313 ASRMLFGLADLGDAPGIFRRLSKSSVPFISLAFTTLLMLLGLVLLFVVPEVMTAFTIVST 372 Query: 378 VSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVLVLLTLED 437 VSAIL +F W+ IL SY+ YRK+RP LH KS+YKMP G LM W +AF FVL LL L Sbjct: 373 VSAILVIFTWSTILASYIAYRKKRPDLHAKSLYKMPGGVLMAWFSLAFLAFVLGLLALRP 432 Query: 438 DTRQALLVTPLWFIALGLGWLF 459 DTR AL V P WFI L + + F Sbjct: 433 DTRLALCVMPAWFIWLWIAYPF 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: 768 Number of extensions: 35 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: 465 Length adjustment: 33 Effective length of query: 437 Effective length of database: 432 Effective search space: 188784 Effective search space used: 188784 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