Align deoxynucleoside transporter, substrate-binding component (characterized)
to candidate SMc02324 SMc02324 periplasmic binding ABC transporter protein
Query= reanno::Burk376:H281DRAFT_01114 (334 letters) >FitnessBrowser__Smeli:SMc02324 Length = 329 Score = 146 bits (369), Expect = 6e-40 Identities = 95/292 (32%), Positives = 156/292 (53%), Gaps = 3/292 (1%) Query: 6 LGAALAAAALTVGVIAAAQAATNETIVTVVKVTGINWFNRMDEGVKEFAKDNPGVTAYQT 65 L + + AA+ V ++A A A N+ I VVK GI +F ++G +E AK+ V T Sbjct: 4 LKSLMVTAAVAVALMANAAHAENKKIALVVKALGIGFFEAANKGAQEAAKELGDVEIIYT 63 Query: 66 GPGRADAAQQLKIIEDLIAKKVNAIAVVPYDPPTLEPALKKAMDRGIKVVTHEADNAK-N 124 GP A Q+++I LIA+KV+AIAV D L PALKKAMDRGIKV++ ++ AK Sbjct: 64 GPTSTTAEGQIEVINSLIAQKVDAIAVSANDTDALVPALKKAMDRGIKVISWDSGVAKEG 123 Query: 125 TMVDIEAFDNTAYGAGLNERLASCMHNEGKWAVLVGSLGSRSQVQWADGGIGNAKAKYAK 184 ++ + + G + + A + G AVL S + +Q W + + Y Sbjct: 124 RLMHLNPSSSPLIGNMIIKLAADNLPEGGDVAVLSASATATNQNTWI-AEMKKVQGNYKG 182 Query: 185 MNLVEPKLETNNDGERAYEVAKEVLRKHPDLKGFQGSSSLDVIGIGRAVEEAGMQGKICV 244 +N+V + ++ +++Y + +++ HP+LK +S+ ++ +AV +AG G+I V Sbjct: 183 INVV-ATVYGDDLADKSYRETQGLIQSHPNLKAIIAPTSVGIVAAAQAVTDAGKIGQINV 241 Query: 245 YGTGLPTEAGKFLESGAINGIAFWDPKLAGIAMNKVAKMLVDGKTVENGADL 296 G GLP+E ++SGA A W+P G + +A L++G + GA+L Sbjct: 242 TGLGLPSEMAGHVKSGASKSFAIWNPIDLGYSATMIAYDLINGAEAKPGAEL 293 Lambda K H 0.314 0.133 0.385 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: 248 Number of extensions: 17 Number of successful extensions: 2 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: 334 Length of database: 329 Length adjustment: 28 Effective length of query: 306 Effective length of database: 301 Effective search space: 92106 Effective search space used: 92106 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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