Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate GFF3102 Psest_3161 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= uniprot:Q31RN9 (396 letters) >FitnessBrowser__psRCH2:GFF3102 Length = 365 Score = 248 bits (633), Expect = 2e-70 Identities = 145/379 (38%), Positives = 218/379 (57%), Gaps = 40/379 (10%) Query: 15 IAWLRQNLFSSWLNSAITLLLVVIIVTVVGRLGLWITTEARWTVLVDNWTLFFVGRYPAA 74 + WLR NLFSSW+N+ +TL+ + ++ +V + W +A WT R + Sbjct: 20 LGWLRANLFSSWINTLLTLVGLYLLWLIVPPVLEWAIFKADWTGET---------RADCS 70 Query: 75 EQWRLWLWLGLLSPTLGLTWGCLATGSHRWQRRSLWGWAGLAAAIAGIPLPWFPHKLGLA 134 + W+++ G RW R W + A A + L PHKL Sbjct: 71 REGACWVFI---QTRFGQFMYGFYPTELRW-RVDAAAWLAIIGA-APLFLRQMPHKLRY- 124 Query: 135 AIAATVPAASWLAQRCRGQAWLRFLPTLWGVLFLVGLWLLQGG-LGLRPVSSNDWSGLLL 193 G +L P L+ WLL GG LGL+ V ++ W GL+L Sbjct: 125 -----------------GIGYLLVYP-------LLAYWLLHGGFLGLQTVPTSQWGGLML 160 Query: 194 TLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQVMVPLM 253 T+ A + + +LPLGILLALGR+S +PAIR L VT+IE +RG+PL+T+LF VM+PL Sbjct: 161 TVVIAAVGIAGALPLGILLALGRRSDMPAIRVLCVTFIEFWRGVPLITVLFMSSVMLPLF 220 Query: 254 LDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTYRFIVL 313 L +D++LRA++ + F +AY+AE VRGGLQAIP+GQ+EAAAA+GL +++ ++L Sbjct: 221 LPEGMNLDKLLRAMLMVVFFEAAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSTLLVIL 280 Query: 314 PQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYLGRYAEVYLFLGVL 373 PQAL++ IP IV F+ L +DT+L+ I+GL + L + A+PA+LG E Y+F ++ Sbjct: 281 PQALKLVIPGIVNTFIALFKDTSLVIIIGLFDFLNSIKRATADPAWLGMSTEGYVFAALV 340 Query: 374 YWLCCYGLAQLSRRLEQRL 392 YW+ C+G+++ S RLE++L Sbjct: 341 YWMFCFGMSRYSMRLERKL 359 Lambda K H 0.329 0.142 0.471 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: 480 Number of extensions: 24 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: 396 Length of database: 365 Length adjustment: 30 Effective length of query: 366 Effective length of database: 335 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 (21.8 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