Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate N515DRAFT_2414 N515DRAFT_2414 simple sugar transport system permease protein
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__Dyella79:N515DRAFT_2414 Length = 358 Score = 95.9 bits (237), Expect = 1e-24 Identities = 88/278 (31%), Positives = 132/278 (47%), Gaps = 22/278 (7%) Query: 45 LGIIAVGMTFVILSGGIDLSVGSVIAFTGVFLAKVIG---DFGLSPL-LAFPLVLVMGCA 100 L ++++GMT VI G+D+SVG+V+A A IG + GL PL LA L G Sbjct: 75 LALVSLGMTLVIALRGLDISVGAVLAIAATVAAWTIGHVSNDGLLPLWLAIAAALAAGAL 134 Query: 101 FGAFMGLLIDALKIPAFIITLAGMFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGG 160 G + G L+ + + TL M RG++ +S I TL + G G Sbjct: 135 CGLWNGWLVVGAGMQPIVATLILMVAGRGIAQSISGGQIL-------TLYYAPYSFLGNG 187 Query: 161 RLSAMGLLMLAVVVIGIF-----LAHRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYM 215 +GL VV +F +T G V AIG N +A++ G+ R+ T+ Y+ Sbjct: 188 --FVLGLPFSLFVVAAVFALLQLALRKTALGLFVRAIGHNPQAAHVAGVRARAITLGAYV 245 Query: 216 LSTGLATLAGIVFSIYTQAGYA-LAGVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAI 274 A LAG++ S + A AG+ +ELDAI +V +GG+LL GG ++ G+L G I Sbjct: 246 FCGIAAALAGLLVSSNVNSADANNAGLLLELDAILAVALGGSLLGGGRFSLAGSLLGALI 305 Query: 275 QGLIQTYINFDGTLSSWWTKIAI-GILLFIFIALQRGL 311 + T I G +A+ +L+F + LQ L Sbjct: 306 IQALTTTIYAIGVPPQ--VNLAVKAVLVFAVMLLQSPL 341 Lambda K H 0.329 0.145 0.428 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: 17 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: 331 Length of database: 358 Length adjustment: 29 Effective length of query: 302 Effective length of database: 329 Effective search space: 99358 Effective search space used: 99358 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