Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_011384984.1 AMB_RS13100 branched-chain amino acid ABC transporter permease
Query= uniprot:G8ALI9 (505 letters) >NCBI__GCF_000009985.1:WP_011384984.1 Length = 320 Score = 107 bits (268), Expect = 5e-28 Identities = 93/324 (28%), Positives = 153/324 (47%), Gaps = 37/324 (11%) Query: 154 IAVVVALAFPFTPLA---DRQLLDIGILLLTY--IMLGWGLNIVVGLAGLLDLGYVAFYA 208 IA +A ++ PLA + ++ + + LT I + W L + L G++ G+ AF+ Sbjct: 7 IAAFLAFSYIAVPLALGSNAYVIGLLVAALTIGGIAVAWAL--LGNLGGMVSFGHAAFFG 64 Query: 209 VGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRI 268 VGAY ALL G+ + + +AG AA++ V P LRLRG YFA+ L + EI RI Sbjct: 65 VGAYVSALLTLRGGWPVFPAMLVAGLGAAIASVAT-MPALRLRGPYFALAILAYAEIFRI 123 Query: 269 ILINWYQFTGGPNGISGIPR-PSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYY 327 + TGG G+ IPR P+ G+ FG + Y+ Sbjct: 124 LATELKPITGGAAGLLSIPRLPNVLGLD----------------FGTKLGG-------YF 160 Query: 328 LILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFA 387 +IL + + +R+ P G A +A+ + + A +G+N T +K ++A G Sbjct: 161 VILTIVVAAMAAYHLIRRSPYGLALKAMHDSEDATRVVGVNSTLLKAWMLVVSAFITGMV 220 Query: 388 GSFFATRQGFISPESFTFIESAIILAIV--VLGGMGSQIGVVVAAFLVIGLPE-AFRE-L 443 G+F A F+ P+ + F LAIV + GG + G +V A +V + + AF+ L Sbjct: 221 GAFNAHYINFLEPD-YAFAGQWTTLAIVSAIFGGYRTVSGPLVGAVVVYLVDQLAFKPIL 279 Query: 444 ADYRMLAFGMGMVLIMLWRPRGLL 467 + G+ + ++L+ P GL+ Sbjct: 280 PQGHQIVLGVLLGAMILFSPGGLM 303 Lambda K H 0.329 0.144 0.438 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: 468 Number of extensions: 50 Number of successful extensions: 5 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: 505 Length of database: 320 Length adjustment: 31 Effective length of query: 474 Effective length of database: 289 Effective search space: 136986 Effective search space used: 136986 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