Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate GFF968 PS417_04910 amino acid ABC transporter permease
Query= uniprot:Q31RN9 (396 letters) >FitnessBrowser__WCS417:GFF968 Length = 365 Score = 254 bits (650), Expect = 2e-72 Identities = 148/398 (37%), Positives = 225/398 (56%), Gaps = 76/398 (19%) Query: 14 PIAWLRQNLFSSWLNSAITLLLVVIIVTVVGRLGLWITTEARWT---------------V 58 P+AW+R NLFSSWLN+ +TLL +I VV + W +A W Sbjct: 19 PMAWMRANLFSSWLNTLLTLLAFYLIYLVVPPILSWAIIDANWVGTTRADCTKEGACWVF 78 Query: 59 LVDNWTLFFVGRYPAAEQWR--LWLWLGLLSPTLGLTWGCLATGSHRWQRRSLWGWAGLA 116 + + F G YP +WR L +WL ++ G R+QR++++G Sbjct: 79 IQQRFGQFMYGYYPGDLRWRVDLTVWLAIV--------GVAPLFISRFQRKAVYG----- 125 Query: 117 AAIAGIPLPWFPHKLGLAAIAATVPAASWLAQRCRGQAWLRFLPTLWGVLF-LVGLWLLQ 175 L FL VL+ ++ +LL Sbjct: 126 ---------------------------------------LGFL-----VLYPIIAFFLLH 141 Query: 176 GGL-GLRPVSSNDWSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELF 234 GG+ GL V+++ W GL+LTL A + + +LPLGI+LALGR+S++PAIR + VT+IE + Sbjct: 142 GGIFGLTNVATSQWGGLMLTLVIATVGIAGALPLGIMLALGRRSNMPAIRVVCVTFIEFW 201 Query: 235 RGLPLVTILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQF 294 RG+PL+T+LF VM+PL L ID++LRA++G+ +F SAY+AE VRGGLQAIP+GQ+ Sbjct: 202 RGVPLITVLFMSSVMLPLFLPEGMGIDKLLRALIGVILFQSAYVAEVVRGGLQAIPKGQY 261 Query: 295 EAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSIL 354 EAAAA+GL +++ ++LPQAL++ IP IV F+ L +DT+L+ I+GL +LL + Sbjct: 262 EAAAAMGLGYWRSMGLVILPQALKMVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAA 321 Query: 355 ANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRL 392 A+P +LG E Y+F +++W+ C+G+++ S LE +L Sbjct: 322 ADPKWLGMATEGYVFAALVFWIFCFGMSRYSIHLEHKL 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: 443 Number of extensions: 15 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