Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate AZOBR_RS25590 AZOBR_RS25590 sugar ABC transporter permease
Query= uniprot:A3DE71 (289 letters) >FitnessBrowser__azobra:AZOBR_RS25590 Length = 277 Score = 158 bits (400), Expect = 1e-43 Identities = 90/285 (31%), Positives = 150/285 (52%), Gaps = 13/285 (4%) Query: 10 MKRKKKIKDTIANIILAILVVLTLGPIVFMVLTSLMDHNAIARGK-WIAPTRFSNYVEVF 68 M K+ I +++ +V + P + ++TSL +A+ + W + +NY +F Sbjct: 1 MDPKRMIGRIAFGLLVLGIVAWAVFPFAWAIVTSLKAGSALFTVEAWPSQPSLANYAAIF 60 Query: 69 QKLPFGIYFRNSLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMF 128 ++ PFG NSL+ S V+ ++L +A LA Y+L + +F G G ++L + P + Sbjct: 61 KEQPFGRNILNSLLAASAVVALSLGLAVLAAYALGRVRFRGRGLLLFVVLGVSMFPQVAV 120 Query: 129 LLPLYLDFVKIKQATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARID 188 L L+ + + L N I LV+ Y F +PF++W++ F +P ELEEAA +D Sbjct: 121 LSGLF------ELVRWLGLYNRIGSLVLSYLIFTLPFTVWVLTTFMRELPKELEEAAMVD 174 Query: 189 GCNKFTAFLRVMLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIRGFIAY 248 G F RV LPL P + AT + F+ AW+E +FA T+P I + Sbjct: 175 GAGPFVIVTRVFLPLMGPALAATGLLAFIAAWNEFLFALTFTLTDDARTVPVAIA--LMS 232 Query: 249 TTARYDL----LMAAGTIVTIPVLIMFFTMQKKFISGMTAGAVKG 289 ++Y+L +MAA +VT+P++ + Q++ +SG+TAGAVKG Sbjct: 233 GASQYELPWGQIMAASVVVTVPLIGLVLLFQRRIVSGLTAGAVKG 277 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: 225 Number of extensions: 6 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: 277 Length adjustment: 26 Effective length of query: 263 Effective length of database: 251 Effective search space: 66013 Effective search space used: 66013 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: 47 (22.7 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