Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >FitnessBrowser__Keio:17511 Length = 356 Score = 355 bits (911), Expect = e-102 Identities = 185/357 (51%), Positives = 254/357 (71%), Gaps = 8/357 (2%) Query: 1 MANLKIKNLQKGFEGFS-IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGT 59 MA LK++ + K ++G + +IK + L+V D EF+V VGPSGCGKSTLLR++AGLE V+ G Sbjct: 1 MAGLKLQAVTKSWDGKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEGD 60 Query: 60 IELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAAR 119 I ++ + +TE+ P R +AMVFQ YALYPHMSV +NM++ L + G+ K ++ ++V EAAR Sbjct: 61 IWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAAR 120 Query: 120 ILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRL 179 ILEL +L+R+P++LSGGQRQRVA+GRAIVR+P +FLFDEPLSNLDA LRVQMRLEL +L Sbjct: 121 ILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQL 180 Query: 180 HKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKM 239 H+ L+ T +YVTHDQVEAMT+A +V+V+NGG EQ+G+P+++Y +PA+LFVA F+G+P M Sbjct: 181 HRRLKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPAM 240 Query: 240 GFLKGKITRVDSQGCEVQLDAGTRVSLPL-GGRHLSVGSAVTLGIRPEHLELAKPGDCAL 298 L G RV+++G +LD G + LPL GG G +TLGIRPEH+ L+ + + Sbjct: 241 NLLTG---RVNNEGTHFELDGG--IELPLNGGYRQYAGRKMTLGIRPEHIALSSQAEGGV 295 Query: 299 QVTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLFDAD 355 + D E LG+D H R + L +R+ G TL LHL HLFD + Sbjct: 296 PMVMDTLEILGADNLAHGRWGE-QKLVVRLAHQERPTAGSTLWLHLAENQLHLFDGE 351 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: 384 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: 356 Length adjustment: 29 Effective length of query: 338 Effective length of database: 327 Effective search space: 110526 Effective search space used: 110526 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