Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 364 bits (935), Expect = e-105 Identities = 189/399 (47%), Positives = 281/399 (70%), Gaps = 6/399 (1%) Query: 4 KLEIKNLYKIFGEHPQRAFKYIEQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLS 63 K+EIK+LY +FG Q+A K +++G +K +IL+ TG ++ VKDA+L+I EGEIFVIMGLS Sbjct: 3 KIEIKDLYLVFGNEKQKALKMLKEGKTKSEILKATGCTVAVKDANLSINEGEIFVIMGLS 62 Query: 64 GSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTV 123 GSGKST++R +NRLI PT G+V+I+G DIAK+SD EL ++RRK++AMVFQ+F L+PH +V Sbjct: 63 GSGKSTLLRCINRLIRPTSGEVIINGTDIAKVSDKELLQIRRKELAMVFQNFGLLPHRSV 122 Query: 124 LDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALAINP 183 L N AFG+EL G+ ER +KA+++++ VGL+ Y + ELSGGM+QRVGLARALA NP Sbjct: 123 LHNIAFGLELQGVKKGEREQKAMESMQLVGLKGYENQMVSELSGGMQQRVGLARALANNP 182 Query: 184 DILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEV 243 ++LLMDEAFSALDPLIR +MQDEL+ LQ+K ++TIVFI+HDL EA+++GDRIAIM++GE+ Sbjct: 183 EVLLMDEAFSALDPLIRVQMQDELLTLQSKMKKTIVFITHDLSEAIKLGDRIAIMKDGEI 242 Query: 244 VQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRTPNGLIRKTPGFGPRSALKLL 303 VQ+GT +EIL PAN YV F VD S++ +A + P ++ + GP ++ + Sbjct: 243 VQIGTSEEILTEPANAYVERFVENVDRSKIITASSVMVDKP--IVARLKKEGPEVLIRKM 300 Query: 304 QDEDREYGYVIERGNKFVGAVSI-DSLKTALTQQQGLDAALIDAPLAVDAQTPLSELLSH 362 ++ + V++ N VG V + D LK Q + +++ + +V T L ++L Sbjct: 301 RERNLTVLPVVDSNNLLVGEVRLNDLLKLRKEQIRSIESVVRHEVHSVLGDTVLEDILPL 360 Query: 363 VGQAPCAVPVVDEDQQYVGIISKGMLL---RALDREGVN 398 + + + VV+E++++ G++ L+ D+E +N Sbjct: 361 MTKTNSPIWVVNENREFEGVVPLSSLIIEVTGKDKEEIN 399 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: 425 Number of extensions: 17 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: 408 Length adjustment: 31 Effective length of query: 369 Effective length of database: 377 Effective search space: 139113 Effective search space used: 139113 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: 50 (23.9 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