Align L-Arginine ABC transporter, periplasmic substrate-binding component (characterized)
to candidate AO356_26125 AO356_26125 ABC transporter substrate-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5660 (257 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_26125 Length = 260 Score = 313 bits (803), Expect = 2e-90 Identities = 155/258 (60%), Positives = 193/258 (74%), Gaps = 1/258 (0%) Query: 1 MKKLVL-LGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCE 59 +K++ L LG ++L A E L+IGIEAAYPPFASK PD +IVGFDYDIG ALC Sbjct: 3 VKRIALNLGFISLLAFGASLQAAESSLRIGIEAAYPPFASKTPDNAIVGFDYDIGQALCA 62 Query: 60 EMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAG 119 EMKV+CVW EQEFDGLIPALKV+K+DA++SSMSIT +R KSVDFT++YY PARLV + G Sbjct: 63 EMKVRCVWQEQEFDGLIPALKVKKVDAVISSMSITPERLKSVDFTDRYYRIPARLVFRKG 122 Query: 120 TQVSDNLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVSAGRLDGTV 179 + +SD A+LKGK IGVQR + +R+ + AP GAE+ YGSQNEI+LD+ GRLD T+ Sbjct: 123 SAISDIPAQLKGKRIGVQRATNFDRYVTDHFAPAGAEVVRYGSQNEIFLDLLGGRLDATM 182 Query: 180 ADATLLDDGFLKTDAGKGFAFVGPAFTDEKYFGDGIGIAVRKGDALKDKINGAITAIREN 239 A + ++D+ LK GK F FVGP FT+E+YFG GIGIAVRK DAL + N A+ IR N Sbjct: 183 ASSVVIDESLLKRPEGKDFEFVGPNFTEEQYFGTGIGIAVRKNDALAGRFNQALATIRAN 242 Query: 240 GKYKQIQDKYFAFDIYGK 257 G Y +I+ KYF FDIYG+ Sbjct: 243 GTYDRIRQKYFDFDIYGE 260 Lambda K H 0.318 0.138 0.396 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: 261 Number of extensions: 10 Number of successful extensions: 1 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: 257 Length of database: 260 Length adjustment: 24 Effective length of query: 233 Effective length of database: 236 Effective search space: 54988 Effective search space used: 54988 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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