Align Inner-membrane translocator (characterized, see rationale)
to candidate N515DRAFT_2414 N515DRAFT_2414 simple sugar transport system permease protein
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Dyella79:N515DRAFT_2414 Length = 358 Score = 107 bits (267), Expect = 4e-28 Identities = 96/320 (30%), Positives = 147/320 (45%), Gaps = 25/320 (7%) Query: 9 LWITASLLLTMFLVGTFQ--------FDGFASGRVVTNLLRDNAFLLITALGMTLVIISG 60 LW +L+L + G F DG G ++ ++ A L + +LGMTLVI Sbjct: 31 LWPLLTLILLLAGNGLFNPGFLALQWRDGHLYGNLI-DIAHRAAPLALVSLGMTLVIALR 89 Query: 61 GIDLSVGAVIALSGVVTSLLITEYQWHPL----LAFVVILPLGTLFGALMGTIIHVYKLQ 116 G+D+SVGAV+A++ V + I L LA L G L G G ++ +Q Sbjct: 90 GLDISVGAVLAIAATVAAWTIGHVSNDGLLPLWLAIAAALAAGALCGLWNGWLVVGAGMQ 149 Query: 117 PFIVTLAGMFLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNG---ALDLSSLIFILF 173 P + TL M RG+A ++S I + + GNG L S + Sbjct: 150 PIVATLILMVAGRGIAQSISGGQIL-------TLYYAPYSFLGNGFVLGLPFSLFVVAAV 202 Query: 174 FVIIAVVMHYTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYT 233 F ++ + + T G V AIG N +A + G+ T+ Y A LAG++ + Sbjct: 203 FALLQLALRKTALGLFVRAIGHNPQAAHVAGVRARAITLGAYVFCGIAAALAGLLVSSNV 262 Query: 234 FSGYALGA-IGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSW 292 S A A + +ELDAI AV +GG+LL GG + G++LG +++ + T I G + Sbjct: 263 NSADANNAGLLLELDAILAVALGGSLLGGGRFSLAGSLLGALIIQALTTTIYAIG-VPPQ 321 Query: 293 WTKIVIGLLLFFFILLQKLL 312 V +L+F +LLQ L Sbjct: 322 VNLAVKAVLVFAVMLLQSPL 341 Lambda K H 0.330 0.145 0.424 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: 326 Number of extensions: 24 Number of successful extensions: 4 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: 320 Length of database: 358 Length adjustment: 28 Effective length of query: 292 Effective length of database: 330 Effective search space: 96360 Effective search space used: 96360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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