Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_011384209.1 AMB_RS09130 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:G8ALI9 (505 letters) >NCBI__GCF_000009985.1:WP_011384209.1 Length = 415 Score = 473 bits (1216), Expect = e-138 Identities = 256/461 (55%), Positives = 313/461 (67%), Gaps = 57/461 (12%) Query: 16 SILKEAAMTAFVALLLTIPLVGLRTVDRPTGLGLETRWNEVAAAVGLVFLGRLGLCLIRE 75 +++ +A + VA + +P++G+R D TGL L R + VA A G V RL + L+R Sbjct: 8 ALVVDALLGGVVAAAMALPMLGVRLEDGSTGLSLSGRLDWVAWAAGSVAGARLLIGLLRL 67 Query: 76 GHAVTVLVLAAAATAAGFFIAMPTEALRVILIAGGAVIAIRAVLAIRTGRSKLSQAERDK 135 G AG ++P +++ G A++A Sbjct: 68 G-------------LAGRGPSLPAPPRAMMVYVGWAMVAF-------------------- 94 Query: 136 RMDHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGL 195 AL PF P + R L+D L+L Y+MLGWGLNIVVGL Sbjct: 95 -----------------------ALILPFLPFSGRNLVDKATLVLIYVMLGWGLNIVVGL 131 Query: 196 AGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYF 255 AGLLDLG+VAFYAVGAYSYALL+ FG SFWVCLPLAG LAA G++LGFPVLRLRGDY Sbjct: 132 AGLLDLGFVAFYAVGAYSYALLSQTFGLSFWVCLPLAGLLAAAFGMVLGFPVLRLRGDYI 191 Query: 256 AIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLE 315 AIVT+G GEI+R++L NW TGGPNGISGI RPS FG++ F P EG+ F E FGL+ Sbjct: 192 AIVTMGLGEIVRVVLQNWQDVTGGPNGISGIERPSLFGLS-FKMVPPEGSQTFAEFFGLD 250 Query: 316 FSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLA 375 +S HR+IFLY+LIL LAL+ N+ T+R+R+LP+GRAWEALRED+IAC SLGIN T +KL+ Sbjct: 251 YSADHRVIFLYFLILALALLTNVITLRIRRLPVGRAWEALREDEIACRSLGINPTLVKLS 310 Query: 376 AFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIG 435 AFA AMF GFAGSFFATRQGFISPESFTFIESA+ILAIVVLGGMGSQIG+V+AA L++G Sbjct: 311 AFATGAMFAGFAGSFFATRQGFISPESFTFIESAVILAIVVLGGMGSQIGIVLAALLLVG 370 Query: 436 LPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILL 476 LPE FREL +RMLAFG MVLIMLW+P GLL+ R+PTI L Sbjct: 371 LPEWFRELQQFRMLAFGGAMVLIMLWKPAGLLSTREPTIRL 411 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: 697 Number of extensions: 36 Number of successful extensions: 3 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: 505 Length of database: 415 Length adjustment: 33 Effective length of query: 472 Effective length of database: 382 Effective search space: 180304 Effective search space used: 180304 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: 51 (24.3 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