Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_011384209.1 AMB_RS09130 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000009985.1:WP_011384209.1 Length = 415 Score = 248 bits (632), Expect = 3e-70 Identities = 154/353 (43%), Positives = 210/353 (59%), Gaps = 46/353 (13%) Query: 8 WIIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVG 67 W + A AL +LP + S G V A L L+YV+L GLNIVVG AGLLDLG+VAFYAVG Sbjct: 89 WAMVAFAL-ILPFLPFS-GRNLVDKATLVLIYVMLGWGLNIVVGLAGLLDLGFVAFYAVG 146 Query: 68 AYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDY 127 AY +AL++ GL S W+ +P+A LLAA FG +LG P L+LRGDY Sbjct: 147 AYSYALLSQTF--------------GL--SFWVCLPLAGLLAAAFGMVLGFPVLRLRGDY 190 Query: 128 LAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDL------GKRL--EVF 179 +AIVT+G GEI+R+ L N ++T GP G+ I+ +FGL G + E F Sbjct: 191 IAIVTMGLGEIVRVVLQNWQ---DVTGGPNGISGIERPSLFGLSFKMVPPEGSQTFAEFF 247 Query: 180 GFDINS---VTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNM 236 G D ++ V Y+L L L +++ +I R++ +GRAW A+REDEIA +++GIN + Sbjct: 248 GLDYSADHRVIFLYFLILALALLTNVITLRIRRLPVGRAWEALREDEIACRSLGINPTLV 307 Query: 237 KLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVL 296 KL AF GA F G +G+ F QGF+SPESF+ +ES +I+A+VVLGG+G G++L A+L Sbjct: 308 KLSAFATGAMFAGFAGSFFATRQGFISPESFTFIESAVILAIVVLGGMGSQIGIVLAALL 367 Query: 297 LSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPSPE 349 L LPE R + R L AM++IML +P GL + E Sbjct: 368 LVGLPEWFR--------------ELQQFRMLAFGGAMVLIMLWKPAGLLSTRE 406 Lambda K H 0.328 0.144 0.430 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: 435 Number of extensions: 19 Number of successful extensions: 4 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: 358 Length of database: 415 Length adjustment: 30 Effective length of query: 328 Effective length of database: 385 Effective search space: 126280 Effective search space used: 126280 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 (21.7 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