Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate GFF2244 HP15_2194 amino acid ABC transporter, permease protein
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__Marino:GFF2244 Length = 362 Score = 377 bits (969), Expect = e-109 Identities = 189/366 (51%), Positives = 250/366 (68%), Gaps = 13/366 (3%) Query: 19 APSLESGAVSWLRKNLFATPKDTALTIISLLILAWLVPPAIQWLFIDAAWSGGGRGVCAT 78 AP V W+R+NLF+ +T LT+ +L V P + W F+DA + G C Sbjct: 9 APKKALRPVKWMRENLFSGWFNTVLTLGVAYLLVTSVGPLLNWFFLDANFVGSDPSACTG 68 Query: 79 LSQGGSQPEGWSGACWAFVNAKFAQFLFGRYPLDERWRPALVGILFVLLLVPMLIPRIPY 138 +GACW F++ + F++G YP + +WR ++ +L + VP I R P Sbjct: 69 -----------AGACWLFISQRLNFFIYGFYPDELQWRVDVMFLLLAVSFVPQFIERFPG 117 Query: 139 KGLNALLLLVALPILSAILLPGGWFGLTYVETPLWGGLMVTLVLSFVGIAVSLPLGILLA 198 + L + LPI+ L+PGG FGL V++ WGGLM+TL+L+++GI SLP+GILLA Sbjct: 118 RKWLGLFGIFGLPIVGYFLIPGGSFGLEEVQSSKWGGLMLTLILAYIGIIASLPIGILLA 177 Query: 199 LGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLFLPQGVTFDKFLRALIGVSLF 258 LGRRS+MP+I+ +C VFIEV R VPLITVLFMASVMLPLFLP+GV F+K RALIG++L+ Sbjct: 178 LGRRSDMPIIRGICVVFIEVWRAVPLITVLFMASVMLPLFLPEGVNFEKLARALIGITLW 237 Query: 259 ASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVIPGIVNTFIGLFK 318 SAYMAEV+RGGLQAIP+GQYE AD+LGL +W+KMG ++LPQALK+VIPGIVNTFI LFK Sbjct: 238 QSAYMAEVIRGGLQAIPRGQYEAADALGLGYWRKMGLVILPQALKMVIPGIVNTFISLFK 297 Query: 319 DTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTGLIFAGFVFWLFCFGMSRYSGFMERL 378 DT+LV IIG+FD+LG V+ +D W + G +F F FW+FCFG+SRYS +ER Sbjct: 298 DTTLVLIIGLFDILGTVQSTVTDPAWQNVA--IEGYVFVAFCFWVFCFGISRYSQNLERK 355 Query: 379 LDRSQR 384 LD + Sbjct: 356 LDTGHK 361 Lambda K H 0.329 0.144 0.454 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: 589 Number of extensions: 25 Number of successful extensions: 3 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: 384 Length of database: 362 Length adjustment: 30 Effective length of query: 354 Effective length of database: 332 Effective search space: 117528 Effective search space used: 117528 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