Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >FitnessBrowser__SynE:Synpcc7942_0248 Length = 396 Score = 254 bits (648), Expect = 4e-72 Identities = 145/397 (36%), Positives = 223/397 (56%), Gaps = 76/397 (19%) Query: 20 VAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTTRADCTKEGACWVFI 79 +AW+R N+FSSW+N+ +TL +I +V L W +A W + Sbjct: 15 IAWLRQNLFSSWLNSAITLLLVVIIVTVVGRLGLWITTEARWT---------------VL 59 Query: 80 QQRFGQFMYGYYPADLRWRVDLTVWLAVI--------GVAPLFISRFPRKAIYG------ 125 + F G YPA +WR L +WL ++ G R+ R++++G Sbjct: 60 VDNWTLFFVGRYPAAEQWR--LWLWLGLLSPTLGLTWGCLATGSHRWQRRSLWGWAGLAA 117 Query: 126 --------------------------------------LSFL-----VLYPISAWCLLHG 142 L FL VL+ + W LL G Sbjct: 118 AIAGIPLPWFPHKLGLAAIAATVPAASWLAQRCRGQAWLRFLPTLWGVLFLVGLW-LLQG 176 Query: 143 GVFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWR 202 G+ GL V+++ W GL+LTL A + +V +LPLGI+LALGR+S++PAIR + VT+IE +R Sbjct: 177 GL-GLRPVSSNDWSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFR 235 Query: 203 GVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYE 262 G+PL+T+LF VM+PL L D++LRA++G+ +F SAY+AE VRGGLQAIP+GQ+E Sbjct: 236 GLPLVTILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFE 295 Query: 263 AAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAAA 322 AAAA+GL +++ ++LPQAL++ IP IV F+ L +DT+L+ I+GL +LL + A Sbjct: 296 AAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILA 355 Query: 323 DPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKL 359 +P +LG E Y+F +++W+ C+G+++ S LE++L Sbjct: 356 NPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRL 392 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: 46 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 365 Length of database: 396 Length adjustment: 30 Effective length of query: 335 Effective length of database: 366 Effective search space: 122610 Effective search space used: 122610 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: 50 (23.9 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