Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate 3606890 Dshi_0320 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__Dino:3606890 Length = 432 Score = 298 bits (763), Expect = 2e-85 Identities = 181/438 (41%), Positives = 245/438 (55%), Gaps = 72/438 (16%) Query: 6 ASFVRASMIEASPAPSLESGAVSWLRKNLFATPKDTALTIISLLILAWLVPPAIQWLFID 65 A+FVR I SP P E G V+WLR NLF + + LT+++ + WL + W+F + Sbjct: 8 AAFVRTEEIPPSPPPVSEVGIVNWLRSNLFYSIPSSILTLLTAAFIYWLSSILMPWMF-N 66 Query: 66 AAWSGGGRGVCATLSQGGSQPEGWSGACWAFVNAKFAQFLFGRYPLDERWRP-------- 117 W C + G G C+A + ++ Q +FG YP +E WR Sbjct: 67 GVWDANSIRDCREILDGAI------GGCFAVIAERWPQLIFGNYPNEEYWRAVLAFVGLF 120 Query: 118 -ALVGILF------------------------------VLLLVPMLIPRIPYKGLN---- 142 AL +LF V+ LV +++ + +K L Sbjct: 121 VALAPVLFFKLPRKMLWFTGLFPFIAYWLIWGGSAWVSVMALVGVVVGYVAFKALEERSF 180 Query: 143 ---------ALLLL------VALPILSAILLPGGWFGLTYVETPLWGGLMVTLVLSFVGI 187 A LL +A+ LS+++ L VE+ GG M+ +L GI Sbjct: 181 FGAIVAALFATLLFWIFISPLAVNALSSVVA----LSLPQVESRFIGGFMINFILGTSGI 236 Query: 188 AVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLFLPQGVTFDK 247 A+SLPLGI LALGR+SN+P+IK +C VFIE IRGVPLIT+LF+ASVML FLP G +FD Sbjct: 237 ALSLPLGIALALGRQSNLPIIKGVCVVFIEFIRGVPLITLLFVASVMLAYFLPPGTSFDL 296 Query: 248 FLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVIP 307 LR +I ++LFASAY+AE +RGGL A+P+GQYE DSLGL +WQ M I+LPQALK+ IP Sbjct: 297 VLRVIIMITLFASAYIAEAIRGGLAALPRGQYEAGDSLGLDYWQSMRLIILPQALKISIP 356 Query: 308 GIVNTFIGLFKDTSLVSIIGMFDLLGIVR-LNFSDTNWATAVTPLTGLIFAGFVFWLFCF 366 IVN IGLFKDT+LVSII MFD+LG+++ S T W L G FAG +F++FC+ Sbjct: 357 SIVNIAIGLFKDTTLVSIISMFDMLGMIQGPILSSTEWFGVYWELLG--FAGVLFFVFCY 414 Query: 367 GMSRYSGFMERLLDRSQR 384 G+S+YS ++ER L R Sbjct: 415 GISQYSQWLERQLATEHR 432 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: 579 Number of extensions: 28 Number of successful extensions: 5 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: 384 Length of database: 432 Length adjustment: 31 Effective length of query: 353 Effective length of database: 401 Effective search space: 141553 Effective search space used: 141553 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