Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__HerbieS:HSERO_RS22750 Length = 377 Score = 361 bits (927), Expect = e-104 Identities = 188/363 (51%), Positives = 246/363 (67%), Gaps = 2/363 (0%) Query: 1 MASVTLRDICKSYDG-TPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGD 59 MA V ++ + K+YDG + ++LDI DGEF V VGPSGCGKSTLLR++ GLE+I+ G+ Sbjct: 1 MAHVNIKQLRKTYDGRADVLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGE 60 Query: 60 LLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAE 119 L I Q VN LPP +R + MVFQSYALYPHM V +NMAFGLK+A K +I R+ A Sbjct: 61 LAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAAA 120 Query: 120 ILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARL 179 IL++D LL+R P++LSGGQRQRVAIGR +VR+P++FLFDEPLSNLDA LRVQ R+EIA+L Sbjct: 121 ILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAKL 180 Query: 180 HQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQM 239 H+++ +T++YVTHDQVEAMTL DKIVV++ G I Q G PL LY P+N FVAGF+GSP+M Sbjct: 181 HRQLAATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPKM 240 Query: 240 NFVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDEADFTFH 299 NF + V +E+ G L VD V+PG +TLG+R E H Sbjct: 241 NFFQGVVTRCDDSGVQVEIAGGLRLLADVDPLGVTPGAAVTLGLRAEQIREGLGDGQPLH 300 Query: 300 GQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFRENGEA 359 G + + E LG+ N LY+TL+ D++ + DGN V G+ A + + HLF G+A Sbjct: 301 GVVNLVEHLGEANFLYVTLDGGHDIV-VRGDGNRNVDIGQPIALSVHSHAFHLFDAQGQA 359 Query: 360 CTR 362 R Sbjct: 360 LRR 362 Lambda K H 0.322 0.139 0.405 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: 422 Number of extensions: 14 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: 371 Length of database: 377 Length adjustment: 30 Effective length of query: 341 Effective length of database: 347 Effective search space: 118327 Effective search space used: 118327 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 (21.9 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