Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate PP_0294 PP_0294 choline / betaine / carnitine ABC transporter - ATP binding subunit
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Putida:PP_0294 Length = 392 Score = 279 bits (713), Expect = 1e-79 Identities = 177/398 (44%), Positives = 248/398 (62%), Gaps = 27/398 (6%) Query: 13 IFGEHPQRAFKYIEQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVR 72 IF P+ A ++QG ++EQIL++TGL +GV+ A+L I +GEI V+MGLSGSGKS+++R Sbjct: 12 IFSNKPREALALLDQGQTREQILKQTGLVVGVEKANLDINKGEICVLMGLSGSGKSSLLR 71 Query: 73 LLNRLIEPTRGQVLIDG----VDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTA 128 +N L +RG++ ++ +DIA S AEL+ +R K+IAMVFQ FALMP +TV +N + Sbjct: 72 CINGLNTVSRGKLFVEHEGKHIDIANCSAAELKMMRTKRIAMVFQKFALMPWLTVRENIS 131 Query: 129 FGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALAINPDILLM 188 FG+E+ G +ERR+ + L VGL + + PDELSGGM+QRVGLARALA++ DILLM Sbjct: 132 FGLEMQGRPEKERRKLVDEKLELVGLTQWRNKKPDELSGGMQQRVGLARALAMDADILLM 191 Query: 189 DEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGT 248 DE FSALDPLIR +QDEL+ LQAK +TIVF+SHDLDEA+++G RIAIM++G ++Q Sbjct: 192 DEPFSALDPLIRQGLQDELLGLQAKLSKTIVFVSHDLDEALKLGTRIAIMKDGRIIQYSK 251 Query: 249 PDEILNNPANDYVRTFFRGVDISQVFSAKDIAR-----RTPNGLIRKTPGFGPRSALKLL 303 P+EI+ NPA++YVRTF + V + + R + NG + PG S L L Sbjct: 252 PEEIVLNPADEYVRTFVAHTNPLNVLCGRSLMRSLDNCKRVNGSVCLDPGID--SWLDLG 309 Query: 304 QDEDREYGYVIERGNKFVGAVSIDSLKTALTQQQGLDAALID-APLAVDAQTPLSELLSH 362 + G ++R + G +D K A G D L++ P V A + E L Sbjct: 310 E------GGALKRARQ--GQNGLDMQKWA----PGQDVELLERRPTVVHADIGMREALQI 357 Query: 363 VGQAPCAVPVVDEDQQYVGIISKGMLLRALDREGVNNG 400 Q + + D D + VGI+ L AL G N+G Sbjct: 358 RYQTGNKLVLQDND-RVVGILGDTELYHAL--LGKNHG 392 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: 447 Number of extensions: 19 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