Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate RR42_RS33780 RR42_RS33780 GABA permease
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Cup4G11:RR42_RS33780 Length = 474 Score = 323 bits (827), Expect = 1e-92 Identities = 174/462 (37%), Positives = 265/462 (57%), Gaps = 9/462 (1%) Query: 6 QQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQL 65 Q GLK GLK RH+ +IALGG IG GLF+GS V+++AGP+ ++ + I G++ ++MR L Sbjct: 9 QSSGLKHGLKQRHMTMIALGGVIGAGLFVGSGVVIKSAGPAAVISFLITGLLVVLVMRML 68 Query: 66 GEMVAQEPVAGSFSHFAYKYWGDFP------GFLSGWNYWVLYVLVSMAELTAVGTYVHY 119 GEM P GSF +A + W D P GFL+GW YW +V+V E A + V + Sbjct: 69 GEMACALPTVGSFYEYAREAWSDRPAMGELAGFLTGWMYWYFWVIVVALEAVAGASLVQF 128 Query: 120 WWPGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHG 179 W PGVP W +LV + NL +VK++GE EFWFA IKV A++ + G ++ Sbjct: 129 WLPGVPAWSISLVLLVMLTLTNLISVKSFGEFEFWFASIKVAAIVVFLFLAGLFVLGMWP 188 Query: 180 GPQASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQ 239 G AS+++L HGGF P+G + T + G E++ I AAE EPQK++ +A + Sbjct: 189 GATASVAHLTVHGGFAPNGIMPVLTGAVAATGFYFGAEIVTIAAAETAEPQKAVARATSS 248 Query: 240 VIYRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVY 299 VI R+L+FY+ S+ +++ L PWN A +P+V + + A ++N VVLTA LS Sbjct: 249 VITRVLVFYVGSVLLVVCLVPWNS-AGIATPYVSALNAMRIPAAAQIMNAVVLTAVLSAL 307 Query: 300 NSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALG 359 NSG+YA+SRML+ L ++G+AP+AL ++ R GVP AI + L + V+++Y+ P + Sbjct: 308 NSGLYASSRMLFALTKRGDAPKALARLSRNGVPVRAILFATLFGYGAVVMSYVSPDKVFA 367 Query: 360 LLMALVVAALVLNWALISLTHLKSR-RAMVAAGETLVFKSFWFPVSNWICLAFMALILVI 418 L+ + + LI+++ L+ R R A L + + FP W+ +A M I+V Sbjct: 368 FLVNSYGTVAIFVYILIAISQLRLRARLEREAPHRLKVRMWAFPYLTWVAIAGMVGIVVA 427 Query: 419 LAMTPGLSVSVLLVPLWLVVMWAGYAFKRRRAAAHVAARVVG 460 +A P +LL L ++ YA R++ H AA +G Sbjct: 428 MAFIPDQRTPLLLGVASLGILVVAYAV-RQQLRKHAAAAPLG 468 Lambda K H 0.327 0.140 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: 502 Number of extensions: 27 Number of successful extensions: 5 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: 461 Length of database: 474 Length adjustment: 33 Effective length of query: 428 Effective length of database: 441 Effective search space: 188748 Effective search space used: 188748 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