Align glutamate-aspartate periplasmic-binding protein (characterized)
to candidate Ac3H11_1954 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
Query= CharProtDB::CH_002441 (302 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1954 Length = 299 Score = 212 bits (540), Expect = 7e-60 Identities = 110/276 (39%), Positives = 164/276 (59%), Gaps = 1/276 (0%) Query: 25 AAPAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQ-KVVGYSQDYSNAIVEAVKKKLNK 83 A+ A + L++++ G +V+ HRESSVPFSY D+Q K VGY+ D + E V+KK K Sbjct: 21 ASVQAATVLERVSAGGKLVIAHRESSVPFSYVDSQSGKPVGYAVDLCLRMAEVVRKKTGK 80 Query: 84 PDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSDTIFVVGTRLLTKKGG 143 D++V+ + +T NRI +++ G D ECGSTTNN ER+++ AF+ F+ G RLL K Sbjct: 81 KDMEVEFVAVTPANRITMIEEGKADMECGSTTNNAERRQKVAFTIPHFITGARLLVKSAS 140 Query: 144 DIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFM 203 I +L K +V T GTT ++ N E+ M + I+ A DH + +E G A AF+ Sbjct: 141 PIDKVEDLNGKKLVSTKGTTPLKAADQANRERLMGITIMEAPDHAKAVEMVEKGEADAFV 200 Query: 204 MDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQVQTSGEAE 263 MDD LL G A P ++VG+ + E ML K+DP+FKKL+D+ + ++ TS + Sbjct: 201 MDDVLLYGLAAGRPDPKALKVVGRFMTTEPLAIMLPKNDPEFKKLVDEEMRRLITSRDIY 260 Query: 264 KWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDK 299 +DKWF PIPP N +N +S ++ +K P D+ Sbjct: 261 PIYDKWFNKPIPPNNTVLNLPVSYLLRDFWKYPTDQ 296 Lambda K H 0.314 0.130 0.366 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: 223 Number of extensions: 9 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: 302 Length of database: 299 Length adjustment: 27 Effective length of query: 275 Effective length of database: 272 Effective search space: 74800 Effective search space used: 74800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 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