Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= uniprot:A0A161GM94 (322 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 162 bits (409), Expect = 1e-44 Identities = 97/315 (30%), Positives = 167/315 (53%), Gaps = 5/315 (1%) Query: 8 LPTARKPLDLRRFLDDWVMLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTM 67 L T + DL F +L + + + + FL+ N + +S GI A M Sbjct: 10 LATDKPRFDLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGM 69 Query: 68 LYCLASGHFDLSVGSV-----IACAGVVAAVVMRDTNSVFLGISAALVMGLIVGLINGIV 122 + + G D++VGS+ IA A VV AVV + + + + ++GL G + G Sbjct: 70 TFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKA 129 Query: 123 IAKLRVNALITTLATMQIVRGLAYIFANGKAVGVSQESFFVFGNGQMFGVPVPILITIVC 182 + L V A I TL M + RG + +G + +++ +G+G++ +PVP++I + Sbjct: 130 VTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALV 189 Query: 183 FLFFGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRM 242 L YT YGR A+GGN EAA L+GVNVD ++A+ G + L+G +L++R+ Sbjct: 190 AAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARL 249 Query: 243 TSGQPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQ 302 S + + G G+EL VI++ V+GG SL+GG G + + G L++ ++ N + + ++ ++ Q Sbjct: 250 GSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQ 309 Query: 303 YVIRGSILLLAVVID 317 V+ G I++ AV D Sbjct: 310 QVVIGLIIVAAVAFD 324 Lambda K H 0.330 0.144 0.420 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: 245 Number of extensions: 14 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: 322 Length of database: 332 Length adjustment: 28 Effective length of query: 294 Effective length of database: 304 Effective search space: 89376 Effective search space used: 89376 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: 48 (23.1 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