Align L-alanine and D-alanine permease (characterized)
to candidate RR42_RS14635 RR42_RS14635 proline-specific permease
Query= reanno::WCS417:GFF1065 (472 letters) >FitnessBrowser__Cup4G11:RR42_RS14635 Length = 466 Score = 515 bits (1326), Expect = e-150 Identities = 250/447 (55%), Positives = 328/447 (73%), Gaps = 4/447 (0%) Query: 11 ETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIM 70 E +QG L+R L RHIR MALG+ IG GLF GSA AI+ AGPA++L+Y+IGG A+ ++M Sbjct: 3 EQSQG--LQRGLSARHIRFMALGSAIGTGLFYGSASAIQTAGPAVLLAYVIGGAAVYMVM 60 Query: 71 RALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFP 130 RALGEMAV NPVAGSF +YA LGPLAGFL GW Y F +V C+A++TA +YMG WFP Sbjct: 61 RALGEMAVRNPVAGSFGQYASTGLGPLAGFLLGWTYAFEMIVVCLADVTAFGIYMGFWFP 120 Query: 131 DTPRWIWALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFG--N 188 D PRWIW L + +G +NL++VK FGE EFW +L+K+ I+AM+ GGV I+ FGFG + Sbjct: 121 DVPRWIWVLGIVFLIGGLNLLSVKVFGELEFWLSLLKVGAIVAMIGGGVAIMLFGFGMAD 180 Query: 189 DGVALGISNLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIG 248 GVA GI NLW HGGFMPNG+ GV+ S +VMFA+ G+E+IG+TAGEA++PQ+ IP AI Sbjct: 181 GGVATGIHNLWTHGGFMPNGIAGVIASFAVVMFAFGGIEIIGITAGEARDPQRVIPRAIN 240 Query: 249 SVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSS 308 +V RILLFYV L V++S+YPW+ IG++GSPFV F RLGI +AA ++N VVI+AA+S+ Sbjct: 241 AVPLRILLFYVLTLAVLMSLYPWHRIGSEGSPFVQIFSRLGIGSAAAVLNIVVISAAVSA 300 Query: 309 CNGGIFSTGRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKVF 368 N IF GRMLY +A QAP FA S GVP +++ FALL GV+LNY++PE VF Sbjct: 301 INSDIFGAGRMLYGMAVQRQAPRIFASVSRKGVPWMTVVVMAFALLAGVVLNYVMPEDVF 360 Query: 369 VWVTSIATFGAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLALAFLLLVVG 428 + SIATF +W WLMILL+Q+ R+ +S AE A LK+ + +PV+ A AF+L + G Sbjct: 361 TLIASIATFATVWVWLMILLSQVALRRRMSRAEVAALKFPVPFWPVAPLAATAFMLFIFG 420 Query: 429 LMAYFPDTRIALYVGPVFLVLLTVLFY 455 ++ +FP TR AL VG V+L+LL V ++ Sbjct: 421 VLGWFPQTRAALLVGAVWLLLLVVAWW 447 Lambda K H 0.328 0.142 0.447 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: 715 Number of extensions: 30 Number of successful extensions: 2 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: 472 Length of database: 466 Length adjustment: 33 Effective length of query: 439 Effective length of database: 433 Effective search space: 190087 Effective search space used: 190087 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