Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate AO353_07790 AO353_07790 choline ABC transporter ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__pseudo3_N2E3:AO353_07790 Length = 392 Score = 284 bits (726), Expect = 4e-81 Identities = 147/285 (51%), Positives = 207/285 (72%), Gaps = 4/285 (1%) Query: 5 LEIKNLYKIFGEHPQRAFKYIEQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSG 64 + N+ IF + P+ A K ++QG++++QIL+KTG +GV+ ASL IE+GEI V+MGLSG Sbjct: 4 IRFDNVDVIFSKDPREALKLLDQGMTRDQILKKTGQIVGVEKASLDIEKGEICVLMGLSG 63 Query: 65 SGKSTMVRLLNRLIEPTRGQVLIDG----VDIAKISDAELREVRRKKIAMVFQSFALMPH 120 SGKS+++R +N L +RG++ ++ +DIA + AEL+ +R K+IAMVFQ FALMP Sbjct: 64 SGKSSLLRCINGLNTVSRGKLFVEHEGRQIDIASCTPAELKMMRTKRIAMVFQKFALMPW 123 Query: 121 MTVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALA 180 +TV +N +FG+E+ G +ERR+ + L VGL + + PDELSGGM+QRVGLARALA Sbjct: 124 LTVRENISFGLEMQGRPEKERRQLVDEKLELVGLTQWRNKKPDELSGGMQQRVGLARALA 183 Query: 181 INPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQN 240 ++ DILLMDE FSALDPLIR +QDEL++LQ K +TIVF+SHDLDEA+++G RIAIM++ Sbjct: 184 MDADILLMDEPFSALDPLIRQGLQDELLELQRKLHKTIVFVSHDLDEALKLGSRIAIMKD 243 Query: 241 GEVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRTPN 285 G ++Q P+EI+ NPA+DYVRTF + V + + R N Sbjct: 244 GRIIQYSKPEEIVLNPADDYVRTFVAHTNPLNVLCGRSLMRTLDN 288 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: 454 Number of extensions: 13 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: 400 Length of database: 392 Length adjustment: 31 Effective length of query: 369 Effective length of database: 361 Effective search space: 133209 Effective search space used: 133209 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