Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 319 bits (818), Expect = 6e-92 Identities = 176/370 (47%), Positives = 243/370 (65%), Gaps = 26/370 (7%) Query: 1 MANLKIKNLQKGF-EGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGT 59 MA +++ L+K + G + E+ D E +V VGPSGCGK+TLLR+IAGLE +SGGT Sbjct: 1 MAKVRLDKLRKVYPNGHVGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGGT 60 Query: 60 IELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAAR 119 + + R + +++P RD+AMVFQ YALYPHM+V +N+ F L L G KAE+E++V+EAAR Sbjct: 61 LSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAAR 120 Query: 120 ILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRL 179 +LEL L+ +P LSGGQRQRVA+GRA+VR+PK+FL DEPLSNLDA LR+ MR+E+ R+ Sbjct: 121 MLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIARI 180 Query: 180 HKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKM 239 H+ L+ATM+YVTHDQ+EAMT+ ++VVLNGG I+Q+ +P++LY PANLFVAGFLG+P M Sbjct: 181 HQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSPAM 240 Query: 240 GFLKGKITRVDSQGCEVQLDAGTRVSLPLGG---RHLSVGSA--------VTLGIRPEHL 288 L+G + R D G ++++P G L G+A + +G+RPE L Sbjct: 241 NLLRGILYR----------DGGWKLAMPQGELVLGELPQGAALEAWRDRDIVVGLRPEDL 290 Query: 289 EL-AKPGDCALQVTADVSERLGSDTFCHVRTASGE-ALTMRVRGDLASRYGETLSLHLDA 346 L A AL +V E +G++ F ++R GE AL R+ G TL Sbjct: 291 LLCADAAGAALAAQLEVVEPVGNEVFLNLR--HGELALVSRMPPRELPAPGSTLHFGFAP 348 Query: 347 QHCHLFDADG 356 + H FDA G Sbjct: 349 ERLHFFDAKG 358 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: 403 Number of extensions: 18 Number of successful extensions: 1 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: 364 Length adjustment: 30 Effective length of query: 337 Effective length of database: 334 Effective search space: 112558 Effective search space used: 112558 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