Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 273 bits (699), Expect = 4e-78 Identities = 156/361 (43%), Positives = 220/361 (60%), Gaps = 21/361 (5%) Query: 4 VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63 + +RD+ ++G V + ++ ++ G+ LV+LG SGCGK+TLL IAGL V+ G I I Sbjct: 3 IEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIA 62 Query: 64 DRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQI 123 +VT P R I MVFQSYAL+P + V +N+ FGLKV K+P EIE+R+KR ++L + Sbjct: 63 GTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLGL 122 Query: 124 QPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSL 183 L KP ELSGG +QRVA+GRA++ + V L DEPLSNLDAKLR+ +R EI L + L Sbjct: 123 SGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRRL 182 Query: 184 KNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFR 243 TMIYVTHDQ+EA+T+ADRI +M+ G I Q P Y P N FVA FIG+P MN Sbjct: 183 GITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIV- 241 Query: 244 GEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPG---QKVVLGLRPEHVKVDEARDGEPTH 300 + P G + + GG L PG + + G+RPE++++ A G+P Sbjct: 242 -PLCPTQGGAALEPGG-----------RLLFPGMDPDRYLFGIRPENLRL--AESGQP-- 285 Query: 301 QAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESENR 360 A+V E +G+D + GQ + VR G+R G+ V L++D G ++FDA ++ R Sbjct: 286 -AMVTGREYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFDARTQER 344 Query: 361 L 361 + Sbjct: 345 V 345 Lambda K H 0.320 0.137 0.392 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: 380 Number of extensions: 15 Number of successful extensions: 2 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: 361 Length of database: 365 Length adjustment: 29 Effective length of query: 332 Effective length of database: 336 Effective search space: 111552 Effective search space used: 111552 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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