Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 158 bits (400), Expect = 2e-43 Identities = 107/288 (37%), Positives = 159/288 (55%), Gaps = 21/288 (7%) Query: 29 FASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSVIAFTGVFLA----KVIGDFG 84 F + R NIL++ + GIIAVGMTFVIL GGID++VGS++AF + A V+GD Sbjct: 46 FLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGP 105 Query: 85 LSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMFFLRGVSYLVSEESIPINHP 144 + L+A + ++G A G G + L +PAFI+TL GM RG + L+++ P Sbjct: 106 ATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGG-----P 160 Query: 145 IYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHR-TRFGNQVYAIGGNATSANLMG 203 I + W G + +++ A+V +A R TR+G QVYA+GGNA +A L G Sbjct: 161 ISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSG 220 Query: 204 ISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGVELDAIASVVIGGTLLSGGVG 263 ++ T +Y + LA L+G + S + A+AG G EL IASVVIGG L+GG G Sbjct: 221 VNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSG 280 Query: 264 TVLGT-----LFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFIFIA 306 V GT L GV GL+ ++ +S+ ++ IG+++ +A Sbjct: 281 GVGGTVLGALLIGVLSNGLVMLHV------TSYVQQVVIGLIIVAAVA 322 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: 318 Number of extensions: 29 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: 332 Length adjustment: 28 Effective length of query: 303 Effective length of database: 304 Effective search space: 92112 Effective search space used: 92112 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