Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 229 bits (585), Expect = 6e-65 Identities = 118/310 (38%), Positives = 186/310 (60%) Query: 13 KSSFSFGRIWDQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCL 72 K+ F F + WD+ G+L+V VL I + F PNF N+ + +IS++ ++A GM F + Sbjct: 13 KAPFDFAKWWDRVGILIVLLVLLILMSTFAPNFNRVDNLLNIARSISVNAILAAGMTFVI 72 Query: 73 ASGDFDLSVASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINAL 132 + DLSV S++A +GV + V + + AG+ +G LCGL+NG + A L + Sbjct: 73 LTSGIDLSVGSIVAVSGVVSVVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPF 132 Query: 133 ITTLATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLN 192 I TL TM +RG+AY I++G+ + SF LG G+P P+ + + ++ +L Sbjct: 133 IVTLGTMTFLRGMAYTITEGQPIVSSSLSFRELGNGYLIGIPIPVIIMLVVYLLAWFILE 192 Query: 193 KTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSI 252 +T FGR+ A+GGN +AARLAGV V R +++++G+ + +AGII A+R+ S QP Sbjct: 193 RTRFGRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQPTAGT 252 Query: 253 GYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILL 312 GYEL I+A VLGG SL GG G+I + G +ILG + + LL++ F Q +++G++++ Sbjct: 253 GYELDAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIVII 312 Query: 313 AAVIFDRYKQ 322 AV D KQ Sbjct: 313 LAVAIDGLKQ 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: 366 Number of extensions: 18 Number of successful extensions: 2 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 Apr 09 2024. 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