Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate H281DRAFT_05890 H281DRAFT_05890 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= uniprot:A3DE71 (289 letters) >FitnessBrowser__Burk376:H281DRAFT_05890 Length = 317 Score = 128 bits (321), Expect = 2e-34 Identities = 71/212 (33%), Positives = 121/212 (57%), Gaps = 7/212 (3%) Query: 77 FRNSLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMFLLPLYLDF 136 F NSL++ +A+ + TLA Y+ +++K P + IL+T+++P + +P+YL + Sbjct: 112 FVNSLVIGFGSTFLAVFLGTLAAYAFSRFKVPLADDLLFFILSTRMMPPIAVAIPIYLMY 171 Query: 137 VKIKQATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARIDGCNKFTAF 196 + L +S G++++Y+A V ++W+++GF IP E EEAA +DG + AF Sbjct: 172 ------RALGLSDSYVGMIVLYTAVNVSLAVWLLKGFMDEIPREYEEAALVDGYTRLQAF 225 Query: 197 LRVMLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIRGFIAYTTARYDLL 256 ++V+LP A+ GI ATAI+ + AW+E FA LL T+P I I + + Sbjct: 226 VKVVLPQAITGIAATAIFCLIFAWNEYAFA-SLLTSGDAQTMPPFIPFIIGEGGQDWPAV 284 Query: 257 MAAGTIVTIPVLIMFFTMQKKFISGMTAGAVK 288 AA T+ +P+LI ++K + G+T GAV+ Sbjct: 285 AAATTLFVVPILIFTVVLRKHLLRGITFGAVR 316 Lambda K H 0.332 0.145 0.434 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: 240 Number of extensions: 12 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: 289 Length of database: 317 Length adjustment: 27 Effective length of query: 262 Effective length of database: 290 Effective search space: 75980 Effective search space used: 75980 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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