Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate HSERO_RS05325 HSERO_RS05325 ribose ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__HerbieS:HSERO_RS05325 Length = 328 Score = 190 bits (483), Expect = 4e-53 Identities = 111/302 (36%), Positives = 176/302 (58%), Gaps = 19/302 (6%) Query: 26 GMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVASVI 85 G++VV ++ +A NF T N + +S+ G++A GM F + +G DLSV + + Sbjct: 35 GLVVVSLLMGLAS----DNFFTLSNWFNVLRQVSIVGILAVGMSFVILTGGIDLSVGAAM 90 Query: 86 ACAGVTTA-VVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIVRG 144 A AG +A +++N + + G+ L GL+NG ++A ++ A+I TLATM + RG Sbjct: 91 ALAGTISAGLIVNSGLPAPLALLCGVGLATCIGLLNGALVAWGRMPAIIVTLATMGVARG 150 Query: 145 LAYIISDGKAV-GIEDESFFALGYANWFGL------PAPIWLTVACLIIFGLLLNKTTFG 197 + I S G + G+ G+ +WFG+ P P+ L + + LLL +T FG Sbjct: 151 VGLIYSGGYPISGLP-------GWISWFGVGRIGMVPVPVILMLIVYALAWLLLQRTAFG 203 Query: 198 RNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELI 257 R+ AIGGNE AARL+GV R K+ ++ +SG S +A IIL R+ SGQP +G+EL Sbjct: 204 RHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELD 263 Query: 258 VISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIF 317 I+A VLGG ++ GG G + + G ++LG + N +NL+ I+P+ Q ++RG+I+L A+ Sbjct: 264 AIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLNLMGINPYLQDIIRGVIILLAIYI 323 Query: 318 DR 319 R Sbjct: 324 AR 325 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: 364 Number of extensions: 27 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 328 Length of database: 328 Length adjustment: 28 Effective length of query: 300 Effective length of database: 300 Effective search space: 90000 Effective search space used: 90000 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