Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate GFF2244 HP15_2194 amino acid ABC transporter, permease protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >FitnessBrowser__Marino:GFF2244 Length = 362 Score = 468 bits (1204), Expect = e-136 Identities = 223/355 (62%), Positives = 275/355 (77%) Query: 10 MPPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTTRADC 69 M P ++ V WMR N+FS W NT+LTL YL+ V PL+ W LDAN+VG+ + C Sbjct: 7 MKAPKKALRPVKWMRENLFSGWFNTVLTLGVAYLLVTSVGPLLNWFFLDANFVGSDPSAC 66 Query: 70 TKEGACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLFISRFPRKAIYGLSFL 129 T GACW+FI QR F+YG+YP +L+WRVD+ L + P FI RFP + GL + Sbjct: 67 TGAGACWLFISQRLNFFIYGFYPDELQWRVDVMFLLLAVSFVPQFIERFPGRKWLGLFGI 126 Query: 130 VLYPISAWCLLHGGVFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNMPA 189 PI + L+ GG FGL+ V +S+WGGLMLTL++A +GI+ +LP+GI+LALGRRS+MP Sbjct: 127 FGLPIVGYFLIPGGSFGLEEVQSSKWGGLMLTLILAYIGIIASLPIGILLALGRRSDMPI 186 Query: 190 IRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILFQSAYIAEVV 249 IR +CV FIE WR VPLITVLFM+SVMLPLFLPEG+NF+KL RALIG+ L+QSAY+AEV+ Sbjct: 187 IRGICVVFIEVWRAVPLITVLFMASVMLPLFLPEGVNFEKLARALIGITLWQSAYMAEVI 246 Query: 250 RGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIG 309 RGGLQAIP+GQYEAA A+GLGYWR MGLVILPQALK+VIPGIVNTFI+LFKDT+LV+IIG Sbjct: 247 RGGLQAIPRGQYEAADALGLGYWRKMGLVILPQALKMVIPGIVNTFISLFKDTTLVLIIG 306 Query: 310 LFDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTGHK 364 LFD+L +V+ DP W +A EGYVF A FW+FCFG+SRYS +LERKLDTGHK Sbjct: 307 LFDILGTVQSTVTDPAWQNVAIEGYVFVAFCFWVFCFGISRYSQNLERKLDTGHK 361 Lambda K H 0.330 0.144 0.469 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: 657 Number of extensions: 37 Number of successful extensions: 1 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: 365 Length of database: 362 Length adjustment: 29 Effective length of query: 336 Effective length of database: 333 Effective search space: 111888 Effective search space used: 111888 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 (21.9 bits) S2: 49 (23.5 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