Align D-serine/D-alanine/glycine transporter (characterized)
to candidate RR42_RS33780 RR42_RS33780 GABA permease
Query= SwissProt::A0A0H2VDI7 (470 letters) >FitnessBrowser__Cup4G11:RR42_RS33780 Length = 474 Score = 296 bits (757), Expect = 1e-84 Identities = 171/475 (36%), Positives = 265/475 (55%), Gaps = 26/475 (5%) Query: 7 VVADDQAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFM 66 ++ Q L+ L RH+ +IA+GG IG GLF+GSG I AGP+ + ++I G + Sbjct: 1 MIHHQQQQQSSGLKHGLKQRHMTMIALGGVIGAGLFVGSGVVIKSAGPAAVISFLITGLL 60 Query: 67 LFFVMRAMGELLLSNLEYKSFSDFASDL------LGPWAGYFTGWTYWFCWVVTGMADVV 120 + VMR +GE+ + SF ++A + +G AG+ TGW YW+ WV+ + V Sbjct: 61 VVLVMRMLGEMACALPTVGSFYEYAREAWSDRPAMGELAGFLTGWMYWYFWVIVVALEAV 120 Query: 121 AITAYAQFWFPGLSDWVASLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAI-VSLIVVG 179 A + QFW PG+ W SL ++++L + NL +VK FGE EFWFA IK+ AI V L + G Sbjct: 121 AGASLVQFWLPGVPAWSISLVLLVMLTLTNLISVKSFGEFEFWFASIKVAAIVVFLFLAG 180 Query: 180 LVMVAMHFQSPTGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETK 239 L ++ M G AS AHL GG+ P G+ G A + G E+V AAET Sbjct: 181 LFVLGMW----PGATASVAHLTVHGGFAPNGIMPVLTGAVAATGFYFGAEIVTIAAAETA 236 Query: 240 DPEKSLPRAINSIPIRIIMFYVFSLIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVI 299 +P+K++ RA +S+ R+++FYV S+++++ + PW+S +P+V + +PAAA ++ Sbjct: 237 EPQKAVARATSSVITRVLVFYVGSVLLVVCLVPWNS-AGIATPYVSALNAMRIPAAAQIM 295 Query: 300 NFVVLTSAASSANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGV 359 N VVLT+ S+ NSG++++SRMLF L + G APKA A+LS+ VP + + F+ + G V Sbjct: 296 NAVVLTAVLSALNSGLYASSRMLFALTKRGDAPKALARLSRNGVPVRAILFATLFGYGAV 355 Query: 360 VMLYVNPSVIGAFTMITTVSAILFMFVWTIILCSYLVYR----KQRPHLHEKSIYKMPLG 415 VM YV+P + AF + + +FV+ +I S L R ++ PH + ++ P Sbjct: 356 VMSYVSPDKVFAF--LVNSYGTVAIFVYILIAISQLRLRARLEREAPHRLKVRMWAFP-- 411 Query: 416 KLMCWVCMAFFVFVLVLLTLEDDTRQALLVTPLWFIALGLGWLFIGKKRAAELRK 470 + WV +A V ++V + D R TPL LG L + +LRK Sbjct: 412 -YLTWVAIAGMVGIVVAMAFIPDQR-----TPLLLGVASLGILVVAYAVRQQLRK 460 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: 619 Number of extensions: 30 Number of successful extensions: 4 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: 474 Length adjustment: 33 Effective length of query: 437 Effective length of database: 441 Effective search space: 192717 Effective search space used: 192717 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