Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate RR42_RS18590 RR42_RS18590 hypothetical protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >FitnessBrowser__Cup4G11:RR42_RS18590 Length = 359 Score = 349 bits (896), Expect = e-101 Identities = 186/358 (51%), Positives = 248/358 (69%), Gaps = 7/358 (1%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTI 60 MA+++I+ +QK F +I+G+D+++ D +F V VGPSGCGKSTLLR+IAGLEE++ G I Sbjct: 1 MASVQIRGIQKYFGSTQVIRGVDIDIADGQFTVLVGPSGCGKSTLLRMIAGLEEITTGEI 60 Query: 61 ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARI 120 + R + + P +RD+AMVFQ YALYPHM+V NM+F+L LA K E+++KV++A+ I Sbjct: 61 AIGNRVVNRLPPKERDIAMVFQNYALYPHMTVYDNMAFSLKLAKGDKEEIKRKVAKASAI 120 Query: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLH 180 L L +LER P+QLSGGQRQRVA+GRAIVR+P++FLFDEPLSNLDA LRVQMR E+ LH Sbjct: 121 LGLDSLLERYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKELH 180 Query: 181 KELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMG 240 + L+ T +YVTHDQ+EAMTMAD++VV+ G++EQ G PL LY P NLFVAGF+G+P M Sbjct: 181 QRLRTTSVYVTHDQIEAMTMADQIVVMRDGRVEQRGKPLALYDHPDNLFVAGFIGSPAMN 240 Query: 241 FLKGKITRVDSQGCEVQLDAGTRVSLP--LGGRHLSVGSAVTLGIRPEHLELAKPGDCAL 298 F+ G + R V+ GTR+ P + G V G+RPEHL L PG L Sbjct: 241 FVPGVLRRSGGDAA-VEFPDGTRLPAPARFDATAGTDGQRVIYGVRPEHLTLGMPGQ-GL 298 Query: 299 QVTADVSERLGSDTFCHVRTASGEALTM-RVRGDLASRYGETLSLHLDAQHCHLFDAD 355 Q V E G++T + R E +++ R R D A+ G+ L+L D QH HLFDAD Sbjct: 299 QTRVSVVEPTGANTEIYSRFCEAEFISIFRERHDFAA--GDILNLVPDHQHTHLFDAD 354 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: 385 Number of extensions: 15 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: 367 Length of database: 359 Length adjustment: 29 Effective length of query: 338 Effective length of database: 330 Effective search space: 111540 Effective search space used: 111540 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 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