Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate H281DRAFT_03228 H281DRAFT_03228 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >FitnessBrowser__Burk376:H281DRAFT_03228 Length = 383 Score = 364 bits (935), Expect = e-105 Identities = 191/372 (51%), Positives = 260/372 (69%), Gaps = 14/372 (3%) Query: 1 MANLKIKNLQKGF-EGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGT 59 MA++ ++ +QK + +G +I+ +DLE+ + EF VF+GPSGCGKSTLLR+IAGLE+++ G Sbjct: 1 MASISLRGVQKAYGDGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60 Query: 60 IELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAAR 119 + + G+ + +V A+R +AMVFQ+YAL+PHM+V +NM+F L LA K E+++KV EAAR Sbjct: 61 LFIGGKVMNDVPAAQRGVAMVFQSYALFPHMTVFENMAFGLKLAKTPKDEIDRKVREAAR 120 Query: 120 ILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRL 179 IL+L +LER+PK LSGGQRQRVAIGRAIVR P +FLFDEPLSNLDA LR Q R+E+ RL Sbjct: 121 ILQLEALLERRPKALSGGQRQRVAIGRAIVRQPGVFLFDEPLSNLDATLRGQTRIEIARL 180 Query: 180 HKEL-QATMIYVTHDQVEAMTMADKVVVLNGGK-------IEQVGSPLDLYHQPANLFVA 231 HK+ +A+++YVTHDQ+EAMT+ADK+V+L+ GK I Q+G+PL+LYH+P + FVA Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPRSRFVA 240 Query: 232 GFLGTPKMGFLKGKITRVDSQGCEVQLD-AGTRVSLPLGGRHLSVGSAVTLGIRPEHLEL 290 GF+G+P+M FL G+I VD+QG V LD V +P G L V AVTLG+RPEHLE Sbjct: 241 GFIGSPRMNFLPGRIASVDAQGVVVTLDHTHENVRVPADGAALQVSQAVTLGVRPEHLEF 300 Query: 291 A----KPGDCALQVTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDA 346 A D L T + E+LG ++ H+ G AL + GD G+ +L + Sbjct: 301 ADLSSSHDDAVLSRTVSLVEQLGEHSYVHLDQPGGVALIAKAPGDTRLAPGDRANLRVPR 360 Query: 347 QHCHLFDADGVA 358 HLF DG A Sbjct: 361 HATHLFTEDGFA 372 Lambda K H 0.320 0.137 0.389 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: 430 Number of extensions: 15 Number of successful extensions: 5 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: 367 Length of database: 383 Length adjustment: 30 Effective length of query: 337 Effective length of database: 353 Effective search space: 118961 Effective search space used: 118961 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 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