Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate AZOBR_RS23480 AZOBR_RS23480 glycine/betaine ABC transporter ATP-binding protein
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__azobra:AZOBR_RS23480 Length = 398 Score = 449 bits (1155), Expect = e-131 Identities = 232/399 (58%), Positives = 305/399 (76%), Gaps = 8/399 (2%) Query: 1 MAIKLEVKNLYKIFGEHPQRAFKYIEKGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIM 60 M K+ V + +IFG HP++A ++ GLSKE+I ++TG ++GV DAS +E GEIFVIM Sbjct: 1 MTAKIAVNGVTRIFGRHPRQALDLLKAGLSKEEIFKRTGQTVGVLDASFEVEAGEIFVIM 60 Query: 61 GLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPH 120 GLSGSGKST+VR+LNRLI+PT G++ IDG DI K+S AEL E+RR+ + MVFQSFAL+PH Sbjct: 61 GLSGSGKSTLVRMLNRLIDPTAGEIRIDGRDITKLSRAELTELRRRDLGMVFQSFALLPH 120 Query: 121 MTVLDNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALA 180 + V +N AFG+E+AG + + RR+KA AL VGL YA ++P ELSGGM+QRVGLARALA Sbjct: 121 LRVWENAAFGLEIAGESLKARRDKAQQALDAVGLGAYAESFPRELSGGMQQRVGLARALA 180 Query: 181 INPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQN 240 P +LLMDEAFSALDPLIRTEMQDEL++LQA+ QRTIVFISHDLDEA+RIGDR+AIM+ Sbjct: 181 NEPSVLLMDEAFSALDPLIRTEMQDELLRLQAERQRTIVFISHDLDEAIRIGDRLAIMEG 240 Query: 241 GEVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRSPVGLIRKTPGFGPRSAL 300 G+++QVG PDEIL PANDYVR+FFR +D++++ +A DIARR V LIR T G GPR+A+ Sbjct: 241 GQIIQVGRPDEILKQPANDYVRSFFRNIDVTKILTAGDIARRDQVTLIRHT-GEGPRAAV 299 Query: 301 KLLQDEDREYGYVIERGNKFVGVVSIDSLKAALSQAQG---IEAALID--DPLVVDAQTP 355 + L++ DRE+GYV + +F GVVS+++L A+ + G ++ AL+ +PL VD P Sbjct: 300 RQLRERDREFGYVQDGRRRFHGVVSVETLVTAIERHNGSATLDEALLPGIEPLPVD--LP 357 Query: 356 LSELLSHVGQAPCAVPVVDEEHQYVGIISKRMLLQALDR 394 + E+L + APC +PVVD + YVG ISK L+ L R Sbjct: 358 MDEVLPRIASAPCPLPVVDGQGAYVGAISKTAYLETLGR 396 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: 473 Number of extensions: 22 Number of successful extensions: 3 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: 398 Length adjustment: 31 Effective length of query: 369 Effective length of database: 367 Effective search space: 135423 Effective search space used: 135423 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