Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate BWI76_RS17840 BWI76_RS17840 sugar ABC transporter permease
Query= uniprot:A3DHA3 (284 letters) >FitnessBrowser__Koxy:BWI76_RS17840 Length = 313 Score = 148 bits (373), Expect = 2e-40 Identities = 94/287 (32%), Positives = 146/287 (50%), Gaps = 6/287 (2%) Query: 2 RHKEALAGYLFSSPYLAGFLIFFAIPSAMSVYYCFTRGVGSF--EFAGLDNFKSVIASNS 59 + K AL +LF +P L F F IP + F + + E+ GLDNF A Sbjct: 26 KRKRALIPWLFLAPALIIFSWFKFIPMIQGLVMSFYKVNFNQPNEWVGLDNFTRAFADAE 85 Query: 60 YRLAVKNTLIFNSVSVPVIMIVSLLLAMLLNKALRGARYFRMFFVLPLVIPVASIILVWQ 119 AV NTL++ V++ I++ LAMLL R R+ R LP V A + +W+ Sbjct: 86 LHAAVVNTLLYVVVTMFAAAILAFFLAMLLEGPARHLRFIRTAIFLPAVTSAAIVAEMWR 145 Query: 120 ITFNEF--GVLNNLLNHFGIAGVEWL-NSKWSIAVLVLLYVWKNCGYNIILFTAGLNSIP 176 I FN GV+N++L+ FG+A +L +S ++ V++LL++WK YN+++F AGL I Sbjct: 146 ILFNPTPNGVVNHILSWFGVADQGFLASSDQALGVIMLLHIWKAVPYNMVIFIAGLAGIS 205 Query: 177 KDYYDAASIDGAGGFKCFTSITLPLLVPTIFFVFIISIINSFKVFREAYLLCGNYPP-LN 235 +D YDAA++DGA + +TLP ++P + V ++S I F+VF E Y G P Sbjct: 206 RDLYDAANVDGASWWNRLRYVTLPGMIPALSVVLMLSFIRGFRVFAEVYATTGGGPSNAT 265 Query: 236 MYMLQHFMNNNFNNLNYQRLSTASLLMELFIVAIVFLMYKIEGRYGK 282 ++ H F +Y S S L+ F V + ++ R + Sbjct: 266 EMVMTHIYKLGFEQFDYGYASAVSFLLFTFTVLLTICHLTLKKRIAR 312 Lambda K H 0.331 0.144 0.444 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: 220 Number of extensions: 9 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: 284 Length of database: 313 Length adjustment: 27 Effective length of query: 257 Effective length of database: 286 Effective search space: 73502 Effective search space used: 73502 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