Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate H281DRAFT_01585 H281DRAFT_01585 amino acid/amide ABC transporter ATP-binding protein 2, HAAT family
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__Burk376:H281DRAFT_01585 Length = 237 Score = 172 bits (435), Expect = 7e-48 Identities = 94/232 (40%), Positives = 141/232 (60%), Gaps = 1/232 (0%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 +L+V GL YG + V EV GE+V+L+G NGAGK+TTMKA+ G L G + + Sbjct: 5 MLKVAGLNAFYGRAHILFDVGLEVGRGEVVALMGRNGAGKSTTMKAVMGLLPRRQGEVIF 64 Query: 69 LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTI 128 G++I + + + G+ VPE R VFA +T+ ENL G ++ A EK+F + Sbjct: 65 RGQNIAALAPYKIARMGMGFVPEDRRVFADLTVMENLDTGRQPPREGAPQWTP-EKLFRL 123 Query: 129 FPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDV 188 FP L E + G MSGGEQQML + R LM P ++LLDEPS G++P++V+++ ++ ++ Sbjct: 124 FPNLGEMPKRPGGQMSGGEQQMLTVSRTLMGNPYLVLLDEPSEGVAPVIVEQMANMILEL 183 Query: 189 YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYL 240 G++I+L EQN A ++DR YV+E G I +G +L ++ VR AYL Sbjct: 184 KREGLSILLSEQNLHFAELVSDRAYVLEKGQIRFSGTIGELASNETVRRAYL 235 Lambda K H 0.317 0.136 0.373 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: 175 Number of extensions: 7 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: 242 Length of database: 237 Length adjustment: 23 Effective length of query: 219 Effective length of database: 214 Effective search space: 46866 Effective search space used: 46866 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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