Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_013402438.1 CALHY_RS02475 sugar ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_000166355.1:WP_013402438.1 Length = 499 Score = 99.4 bits (246), Expect = 2e-25 Identities = 81/275 (29%), Positives = 136/275 (49%), Gaps = 21/275 (7%) Query: 4 QSMTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTP 63 +S T + LL + +T F G VA++DVSFS N EI AI+G NGAGK+TL N I+G P Sbjct: 2 KSSTDSELLRLHGITKIFPGTVALSDVSFSVNKAEIHAIVGENGAGKSTLMNIISGSLLP 61 Query: 64 TVGRLTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIR 123 G + L +GK+ + R P R +Q ++ Q + L ++V EN+ + + + Sbjct: 62 DKGEIYL---EGKKVNI-RSP--RDAQNLGISIVHQELALCPHLTVAENIYIGRLPE--- 112 Query: 124 ASGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAM 183 A ++ + +E + L D V + + NL Q+ +EIA+A+ Sbjct: 113 ----KSAKIVDFKKLNQMSQEVLSL----FDEVNIKPTD--KVANLNVAQQQIVEIAKAI 162 Query: 184 CTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLD 243 +L LDEP + L+ ++ L ++ ++ + I +L I H + + ++D + VL Sbjct: 163 TFNCKLLILDEPTSALSEADAAVLFKIIKDLKAK-GISILYISHRLREIFELADRITVLR 221 Query: 244 YGRKISDGDPAFVKNDPAVIRAYLGEEEDEELPPE 278 GR I+ + A N V+ +G E E PP+ Sbjct: 222 DGRYITTLNTA-ETNPDQVVSLMVGREIKEMYPPK 255 Score = 52.0 bits (123), Expect = 3e-11 Identities = 54/221 (24%), Positives = 102/221 (46%), Gaps = 18/221 (8%) Query: 27 VNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLRHADGKEFLLERMPGY 86 V +VSF+ + GEI G G+G+T L I G G + L +GK+ + Sbjct: 274 VQNVSFALHEGEILGFAGLVGSGRTELAQTICGILPKHCGEIYL---EGKKIEINSFEDA 330 Query: 87 RISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAGLLGLPSYTRTEREAV 146 + V + LF + V N + A H K + LL ++ + Sbjct: 331 IRHKIGYVTEDRKQYGLFLKLPVAHN-VSAIHLK------YDYKRLL------IDRQKEL 377 Query: 147 DLAKYWLDRVRLLEFADWE-AGNLPYGAQRRLEIARAMCTEPVMLCLDEPAAGLNPRESG 205 LA+ ++ ++ + + + +L G Q+++ IA+ + +P +L LDEP G++ Sbjct: 378 SLAQEFVKKLNVKTSSYVQLVMSLSGGNQQKVMIAKWLAIKPRILILDEPTRGIDVGAKA 437 Query: 206 ELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGR 246 E+ LL + ++ IG++LI ++ ++ + D V+V+ GR Sbjct: 438 EIHSLLRELA-KNGIGIILISSELPEIIGMCDRVLVMREGR 477 Lambda K H 0.319 0.137 0.397 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: 270 Number of extensions: 12 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: 294 Length of database: 499 Length adjustment: 30 Effective length of query: 264 Effective length of database: 469 Effective search space: 123816 Effective search space used: 123816 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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