Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate AO353_12265 AO353_12265 hypothetical protein
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12265 Length = 274 Score = 312 bits (800), Expect = 6e-90 Identities = 157/263 (59%), Positives = 205/263 (77%) Query: 2 AIKLEIKNLYKIFGEHPQRAFKYIEQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMG 61 A K+E+KN++KIFG+ A I Q SK+Q+L +TG +GV D SL+I GEIFVIMG Sbjct: 4 AAKIEVKNVFKIFGDRSADALDMIRQNKSKDQVLAETGCVIGVNDLSLSIATGEIFVIMG 63 Query: 62 LSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHM 121 LSGSGKST+VR +NRLI+PT G +L+DGVDI + LRE RR KI+MVFQSF L+PH Sbjct: 64 LSGSGKSTLVRHINRLIDPTSGVILVDGVDILQYDMEALREFRRHKISMVFQSFGLLPHK 123 Query: 122 TVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALAI 181 VLDN A+G+++ G + + E+A + VGL+ Y + YP +LSGGMRQRVGLARALA Sbjct: 124 NVLDNVAYGLKVRGESKQVCAERAQHWINTVGLQGYENKYPHQLSGGMRQRVGLARALAA 183 Query: 182 NPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNG 241 + DI+LMDEAFSALDPLIR EMQD+L++LQ +TIVFI+HDLDEA+RIG+RIAI+++G Sbjct: 184 DTDIILMDEAFSALDPLIRAEMQDQLLELQQTLHKTIVFITHDLDEAVRIGNRIAILKDG 243 Query: 242 EVVQVGTPDEILNNPANDYVRTF 264 +++QVGTP EIL++PA++YV F Sbjct: 244 QLIQVGTPKEILHSPADEYVDRF 266 Lambda K H 0.319 0.137 0.378 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: 330 Number of extensions: 15 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: 400 Length of database: 274 Length adjustment: 28 Effective length of query: 372 Effective length of database: 246 Effective search space: 91512 Effective search space used: 91512 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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