Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__ANA3:7024902 Length = 320 Score = 132 bits (331), Expect = 2e-35 Identities = 100/322 (31%), Positives = 163/322 (50%), Gaps = 39/322 (12%) Query: 50 PEWFTVALIVVTCLIVGAINPRFFQFAT---LFDLLHSATTMSLFALGTLVVLASGGIDV 106 P W T +L++ T +VG +F FA+ + +LL + + ALG +V+ SGGID+ Sbjct: 8 PLWITASLLL-TMFLVGTF--QFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDL 64 Query: 107 SFTAIAALTMYGITKAV----FAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSL 162 S A+ AL+ G+ ++ + W P F +IL G L G ++G + +H K Sbjct: 65 SVGAVIALS--GVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTI----IHVYKLQPF 118 Query: 163 IVTIGTQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLP------VS 216 IVT+ +L RGL T + ++ P FY + LP +S Sbjct: 119 IVTLAGMFLARGLATTLSEESIAIDHP------------FYDAVAEMSIALPGNGALDLS 166 Query: 217 VLALVAAAVVTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAG 276 L + V+ +++ T G VYA+GG+ AE +G ++ + ++ + LA +AG Sbjct: 167 SLIFILFFVIIAVVMHYTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAG 226 Query: 277 ILHVSNNRLANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILV 336 I+ +G ELD IAAV++GG +TGG+G V+GT+LGV+L+ +I++ + Sbjct: 227 IVFTFYTFSGYALGAIGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFD 286 Query: 337 G-VPSTWQKVIIGA----FILL 353 G + S W K++IG FILL Sbjct: 287 GSLSSWWTKIVIGLLLFFFILL 308 Lambda K H 0.328 0.141 0.426 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: 310 Number of extensions: 19 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: 364 Length of database: 320 Length adjustment: 29 Effective length of query: 335 Effective length of database: 291 Effective search space: 97485 Effective search space used: 97485 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 (21.7 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