Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate WP_011840330.1 RSPH17029_RS02010 amino acid ABC transporter permease
Query= reanno::Smeli:SMc02120 (384 letters) >NCBI__GCF_000015985.1:WP_011840330.1 Length = 442 Score = 286 bits (732), Expect = 8e-82 Identities = 177/436 (40%), Positives = 245/436 (56%), Gaps = 63/436 (14%) Query: 8 FVRASMIEASPAPSLESGAVSWLRKNLFATPKDTALTIISLLILAWLVPPAIQWLFIDAA 67 FVR +M+ P+ E+G VSW+R+NLF+ P + ALT++ L+ + +++ + WL + + Sbjct: 11 FVRETMLPPVAPPANEAGVVSWMRQNLFSGPLNIALTLLGLVAIYYVLEGIVPWL-MRSV 69 Query: 68 WSGGGRGVCATLSQGGSQPEGWSGACWAFVNAKFAQFLFGRYPLDERWRPALVGILFVLL 127 W+ C + EG +GACWA + ++ QFL+G YP WRP L +L + Sbjct: 70 WTADTLAQCRQIITE-RWGEGATGACWAVIRERWPQFLYGFYPNHLYWRPTLTFLLLFVA 128 Query: 128 LVPMLIPRIPYKGL--------NALLLL----VALPILSAILLPGGW--------FG--- 164 L P+L ++P + L A LL + LP+++A GW FG Sbjct: 129 LAPILFAQVPRQMLWFSLAYPFLAFWLLWGGSIFLPLVAAAGFLFGWLAYRLAARFGTIA 188 Query: 165 --------------------------LTYVETPLW---------GGLMVTLVLSFVGIAV 189 LT PLW GG ++ + + GIA+ Sbjct: 189 AVAAAALVPVLWWLFLAGDVSDDLARLTGRTFPLWLEEVRSDKFGGFVLAVTIGVSGIAL 248 Query: 190 SLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLFLPQGVTFDKFL 249 SLPLGI+LALGRRS+M +IK L FIE IRGVPLI +LF AS++L FLP G TFD L Sbjct: 249 SLPLGIILALGRRSDMFLIKALSVSFIEFIRGVPLIALLFTASLLLNYFLPPGTTFDIIL 308 Query: 250 RALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVIPGI 309 R +I V+LFA+AY+AEV+RGGL A+P+GQYE AD+LGL +W+ I+LPQALK+ IPGI Sbjct: 309 RVIIMVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWKAQRLIILPQALKISIPGI 368 Query: 310 VNTFIGLFKDTSLVSIIGMFD-LLGIVRLNFSDTNWATAVTPLTGLIFAGFVFWLFCFGM 368 V+TFIG+FKDT+LV +G+ D L GI + T+W IF G +F+ F F M Sbjct: 369 VSTFIGMFKDTTLVVFVGLLDPLKGITDAVRASTDWKGIY--WEPYIFVGLIFFAFNFAM 426 Query: 369 SRYSGFMERLLDRSQR 384 SRYS +ER L R Sbjct: 427 SRYSMHLERRLKTDHR 442 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: 601 Number of extensions: 29 Number of successful extensions: 4 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: 442 Length adjustment: 31 Effective length of query: 353 Effective length of database: 411 Effective search space: 145083 Effective search space used: 145083 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 Apr 10 2024. 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