Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate AO356_20255 AO356_20255 arabinose ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20255 Length = 322 Score = 384 bits (987), Expect = e-111 Identities = 193/304 (63%), Positives = 238/304 (78%) Query: 20 RIWDQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDL 79 R D + ML+ +F+ C + + NF + +NM+GLGLAIS +G+ AC ML+CLASG FDL Sbjct: 19 RFLDDWVMLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDL 78 Query: 80 SVASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATM 139 SV SVIACAGV AVV+ T S+++GV+A L +G++ GL+NG VIAKL++NALITTLATM Sbjct: 79 SVGSVIACAGVVAAVVMRDTNSVFLGVSAALAMGLIVGLINGIVIAKLRVNALITTLATM 138 Query: 140 QIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRN 199 QIVRGLAYI ++GKAVG+ ESFF G FG+P PI +T+AC + FG LLN TT+GRN Sbjct: 139 QIVRGLAYIFANGKAVGVSQESFFVFGNGQLFGVPVPILITIACFLFFGWLLNYTTYGRN 198 Query: 200 TLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVI 259 T+AIGGN+EAA LAGV V RTKIIIF + GL+ A+AG+ILASRMTSGQPM G+EL VI Sbjct: 199 TMAIGGNQEAALLAGVNVDRTKIIIFAVHGLIGALAGVILASRMTSGQPMIGQGFELTVI 258 Query: 260 SACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDR 319 SACVLGGVSL GGIG I +V+AG+LIL +ENAMNL NI F QYV+RG ILL AV+ DR Sbjct: 259 SACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDR 318 Query: 320 YKQK 323 KQ+ Sbjct: 319 LKQR 322 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: 419 Number of extensions: 14 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: 322 Length adjustment: 28 Effective length of query: 300 Effective length of database: 294 Effective search space: 88200 Effective search space used: 88200 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: 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