Align L-alanine and D-alanine permease (characterized)
to candidate RR42_RS33780 RR42_RS33780 GABA permease
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__Cup4G11:RR42_RS33780 Length = 474 Score = 343 bits (881), Expect = 6e-99 Identities = 185/474 (39%), Positives = 276/474 (58%), Gaps = 18/474 (3%) Query: 9 HGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILV 68 H + Q LK L +RH+ ++ALG IG GLF+GS I+ AGPA ++S++I GL +++ Sbjct: 4 HQQQQQSSGLKHGLKQRHMTMIALGGVIGAGLFVGSGVVIKSAGPAAVISFLITGLLVVL 63 Query: 69 IMRALGEMAVHNPVAGSFSRYAQDY------LGPLAGFLTGWNYWFLWLVTCVAEITAVA 122 +MR LGEMA P GSF YA++ +G LAGFLTGW YW+ W++ E A A Sbjct: 64 VMRMLGEMACALPTVGSFYEYAREAWSDRPAMGELAGFLTGWMYWYFWVIVVALEAVAGA 123 Query: 123 VYMGIWFPDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGII 182 + W P VP W +L LV + NLI+VK+FGEFEFWFA IK+ I+ + G+ Sbjct: 124 SLVQFWLPGVPAWSISLVLLVMLTLTNLISVKSFGEFEFWFASIKVAAIVVFLFLA-GLF 182 Query: 183 AFGFGNDGVALGISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKT 242 G G +++L HGGF PNG+ VL Y G E++ + A E PQK Sbjct: 183 VLGMW-PGATASVAHLTVHGGFAPNGIMPVLTGAVAATGFYFGAEIVTIAAAETAEPQKA 241 Query: 243 IPNAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVI 302 + A SV R+L+FYVG++ +++ + PWN G +P+V + I AA I+N VV+ Sbjct: 242 VARATSSVITRVLVFYVGSVLLVVCLVPWNSAGI-ATPYVSALNAMRIPAAAQIMNAVVL 300 Query: 303 TAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYL 362 TA LS+ N G++++ RML++L + G AP A+ S NGVP RA+L + V+++Y+ Sbjct: 301 TAVLSALNSGLYASSRMLFALTKRGDAPKALARLSRNGVPVRAILFATLFGYGAVVMSYV 360 Query: 363 VPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAF 422 P+KVF ++ + AI+ +++I ++QL+ R L LK RMW +P +++A+A Sbjct: 361 SPDKVFAFLVNSYGTVAIFVYILIAISQLRLRARLEREAPHRLKVRMWAFPYLTWVAIAG 420 Query: 423 LVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYTFKLQ--------PTGDVQRA 468 +V +V MA+ PD R L +G A L +L V+ Y + Q P G+V+RA Sbjct: 421 MVGIVVAMAFIPDQRTPLLLGVASLGIL-VVAYAVRQQLRKHAAAAPLGEVRRA 473 Lambda K H 0.328 0.142 0.444 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: 609 Number of extensions: 18 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: 473 Length of database: 474 Length adjustment: 33 Effective length of query: 440 Effective length of database: 441 Effective search space: 194040 Effective search space used: 194040 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 (21.7 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