Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 160 bits (406), Expect = 3e-44 Identities = 95/303 (31%), Positives = 161/303 (53%), Gaps = 6/303 (1%) Query: 29 VVFAVLFIAC-AIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVASVIAC 87 ++F +L +A F T N + +S+ G++A GM F + G D++V S++A Sbjct: 29 ILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAF 88 Query: 88 AGVTTAVVINLT----ESLW-IGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIV 142 A + A V+ + W I + L+G+ G V G + L + A I TL M + Sbjct: 89 ASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVW 148 Query: 143 RGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLA 202 RG +++DG + ++++ G LP P+ + + L T +GR A Sbjct: 149 RGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYA 208 Query: 203 IGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISAC 262 +GGN EAARL+GV V ++ + G ++ ++G +L++R+ S + + GYEL VI++ Sbjct: 209 VGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASV 268 Query: 263 VLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRYKQ 322 V+GG SL GG G + V G L++G + N + +L+++ + Q VV GLI++AAV FD Y + Sbjct: 269 VIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHYAR 328 Query: 323 KAK 325 K Sbjct: 329 THK 331 Lambda K H 0.327 0.141 0.414 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: 327 Number of extensions: 22 Number of successful extensions: 1 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: 328 Length of database: 332 Length adjustment: 28 Effective length of query: 300 Effective length of database: 304 Effective search space: 91200 Effective search space used: 91200 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