Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate Pf6N2E2_4681 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1)
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4681 Length = 392 Score = 285 bits (728), Expect = 2e-81 Identities = 172/396 (43%), Positives = 252/396 (63%), Gaps = 37/396 (9%) Query: 13 IFGEHPQRAFKYIEKGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVR 72 IF P+ A ++KGLS+ +IL++TGL +GV+ ASL+IE+GEI V+MGLSGSGKS+++R Sbjct: 12 IFSNRPKAALDLLDKGLSRPEILQQTGLIVGVEKASLSIEKGEICVLMGLSGSGKSSLLR 71 Query: 73 LLNRLIEPTRGQVLIDG----VDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTA 128 +N L +RG++ ++ +DIA S AEL+ +R K+IAMVFQ FALMP +TV +N + Sbjct: 72 CINGLNTVSRGKLFVEHEGRQIDIASCSPAELKMMRTKRIAMVFQKFALMPWLTVRENIS 131 Query: 129 FGMELAGIAAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAINPDILLM 188 FG+E+ G +ERR+ + L VGL + + PDELSGGM+QRVGLARALA++ DILLM Sbjct: 132 FGLEMQGRPEKERRKLVDEKLELVGLTQWRNKKPDELSGGMQQRVGLARALAMDADILLM 191 Query: 189 DEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGT 248 DE FSALDPLIR +QDEL++LQ K Q+TIVF+SHDLDEA+++G RIAIM++G+++Q Sbjct: 192 DEPFSALDPLIRQGLQDELLELQRKLQKTIVFVSHDLDEALKLGTRIAIMKDGKIIQYSK 251 Query: 249 PDEILNNPANDYVRTFFRGVDISQVFSAKDIARRSPVGLIRKTPGFGPRSALKLLQDEDR 308 P+EI+ NPA+DYVRTF +A +P+ ++ RS ++ L + R Sbjct: 252 PEEIVLNPADDYVRTF--------------VAHTNPLNVL------CGRSLMRTLDNCKR 291 Query: 309 EYGYVI--ERGNKFVGVVSIDSLK------AALSQAQGIEAALIDD----PLVVDAQTPL 356 G V G+ ++ + +++K AAL + ++D P +VD+ + Sbjct: 292 INGSVCLDPGGDSWLDLAEGNTIKGARQNGAALDLQNWVPGQAVEDLGRRPTLVDSNIGM 351 Query: 357 SELLSHVGQAPCAVPVVDEEHQYVGIISKRMLLQAL 392 + L Q + V+ + Q VGI+ L AL Sbjct: 352 RDALQIRYQTGNKL-VLHDNQQVVGILGDSELYHAL 386 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: 456 Number of extensions: 17 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 (21.8 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