Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 281 bits (718), Expect = 3e-80 Identities = 163/378 (43%), Positives = 231/378 (61%), Gaps = 20/378 (5%) Query: 4 LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63 +E+R+V K YG ++ + +++G+ L+++GPSGCGK+TL+ IAGLE ++ G I Sbjct: 3 IEIRDVRKDYGR--VQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIH 60 Query: 64 VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123 + D++ + P R+I+MVFQSYAL+P ++VR+NI FGLK+RK+P EI+ + RV LL Sbjct: 61 IAGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLL 120 Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 + L KPG+LSGG QQRVA+GRA+ + L DEPLSNLDAKLR MR E+ + + Sbjct: 121 GLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQR 180 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243 RL T +YVTHDQ+EAMT+ D++ +M+DG I Q +P++ Y PAN FVA FIG+PPMN Sbjct: 181 RLGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNI 240 Query: 244 IPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANGLPT 303 +PL + G A L+ G R P G++ + GIRPE + LA +G P Sbjct: 241 VPL-CPTQGG---AALEPG-GRLLFP------GMDPDRYLFGIRPENLRLAE---SGQP- 285 Query: 304 IRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDAKTGE 363 A V E G DT V ++ +V R G + L +DP V LFDA+T E Sbjct: 286 --AMVTGREYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFDARTQE 343 Query: 364 RLGVAGVPKAEAHADNVA 381 R+ + VP + +N A Sbjct: 344 RVD-SVVPARKEGRENPA 360 Lambda K H 0.319 0.138 0.393 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: 420 Number of extensions: 23 Number of successful extensions: 3 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: 386 Length of database: 365 Length adjustment: 30 Effective length of query: 356 Effective length of database: 335 Effective search space: 119260 Effective search space used: 119260 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 (21.7 bits) S2: 50 (23.9 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