Align L-alanine and D-alanine permease (characterized)
to candidate Pf6N2E2_4195 transport permease protein of gamma-aminobutyrate
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4195 Length = 464 Score = 313 bits (801), Expect = 1e-89 Identities = 164/445 (36%), Positives = 265/445 (59%), Gaps = 9/445 (2%) Query: 12 TAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMR 71 T L++ L RH+ ++++ IG GLF+GS AI AGPA++L+Y G ++++MR Sbjct: 4 TQTSNHLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGALVVLVMR 63 Query: 72 ALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPD 131 LGEMAV +P GSFS YA +G AGF GW YW+ W++ E A A + WFP+ Sbjct: 64 MLGEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPN 123 Query: 132 VPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIA-FGFGNDG 190 V W + L + + NL +VK +GEFEFWFAL+K+V II + G+G++A FG Sbjct: 124 VAIWAFTLVITLLLTVTNLFSVKNYGEFEFWFALVKVVAIIGFI--GLGVMAIFGVLPTS 181 Query: 191 VALGISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSV 250 G+S+L+ GF+PNG+ VL ++ MF+++G E++ + A E+KNP + I A SV Sbjct: 182 QVSGVSHLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSV 241 Query: 251 FWRILLFYVGALFVILSIYPWNE--IGTQGSPFVMTFERLGIKTAAGIINFVVITAALSS 308 WRI LFY+ ++F+++++ PWN+ + + GS + ER+GI A I++ VV+ A S Sbjct: 242 IWRIGLFYLVSIFIVVALVPWNDPLLASVGS-YQTVLERMGIPNAKLIVDIVVLVAVTSC 300 Query: 309 CNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVF 368 N +++ RM++SL + G APA +T+ +G P A++LS A L V NY+ P VF Sbjct: 301 LNSALYTASRMMFSLGKRGDAPAVSQRTNKSGTPYWAVMLSTGAAFLAVFANYVAPAAVF 360 Query: 369 VWVTSIATFGAIWTWVMILLAQLKFRKS-LSASERAALKYRMWLYPVSSYLALAFLVLVV 427 ++ + + A+ +++I ++QL+ RK ++ E+ A + MWL+P +Y + F+V + Sbjct: 361 DFLLASSGAIALLVYLVIAVSQLRMRKQRMARGEKVA--FSMWLFPGLTYAVIVFIVGAL 418 Query: 428 GLMAYFPDTRVALYVGPAFLVLLTV 452 +M + RV + VL+ + Sbjct: 419 TIMLFQEAHRVEILATGLLSVLVVI 443 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: 602 Number of extensions: 34 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: 464 Length adjustment: 33 Effective length of query: 440 Effective length of database: 431 Effective search space: 189640 Effective search space used: 189640 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