Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate HSERO_RS03645 HSERO_RS03645 ribose ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__HerbieS:HSERO_RS03645 Length = 339 Score = 192 bits (487), Expect = 1e-53 Identities = 111/303 (36%), Positives = 177/303 (58%), Gaps = 7/303 (2%) Query: 27 MLVVFAVLFIACAIFVP-----NFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSV 81 +LVV +LF +++ NFA+ N + ++++ ++A GM F + + DLSV Sbjct: 32 VLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSV 91 Query: 82 ASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQI 141 SV+A + V + ++L + + + G++ G+VNG ++A L INA + TL TM Sbjct: 92 GSVLAVSAVL-GMQVSLGAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTA 150 Query: 142 VRGLAYIISDGKAVGIED-ESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNT 200 RG AY+++DG V D SF +G ++ +P IW+ VA +++ ++L KT G + Sbjct: 151 FRGAAYLLADGTTVLNNDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHI 210 Query: 201 LAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVIS 260 AIGGN +AARL G+ V + ++ +SGL S +AG + ASR+ GYEL I+ Sbjct: 211 YAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIA 270 Query: 261 ACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRY 320 A VLGG SL GG+G I V G LI+G + N + +L +S F QYV +G +++ AVI D++ Sbjct: 271 AVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKW 330 Query: 321 KQK 323 +QK Sbjct: 331 RQK 333 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: 300 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: 328 Length of database: 339 Length adjustment: 28 Effective length of query: 300 Effective length of database: 311 Effective search space: 93300 Effective search space used: 93300 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