Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_090272108.1 BLU11_RS03755 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ1 (236 letters) >NCBI__GCF_900105005.1:WP_090272108.1 Length = 256 Score = 125 bits (314), Expect = 8e-34 Identities = 77/248 (31%), Positives = 136/248 (54%), Gaps = 16/248 (6%) Query: 1 MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60 +L VSG+ +G + A+ V +++ G+IVSLIG NGAGK+T+ + G + G I F Sbjct: 6 LLDVSGLCMRFGGLLAVDQVALQVEEGQIVSLIGPNGAGKTTVFNCLTGFYKPSAGSIRF 65 Query: 61 EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENL-----------QMGSITAKPGSF 109 G++++ MP ++L R+G+ ++ + R+F +MSV+ENL + + P Sbjct: 66 HGEEVSGMPGFKLARMGMVRTFQHVRLFKQMSVVENLLVAQHHHMNTNMLAGLLKTPSFR 125 Query: 110 ANE---LERVLTLFPR--LKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGL 164 +E L+R R L E ++ AGT++ G+Q+ L I R +++QPRLL+LDEP+ GL Sbjct: 126 RSEKEALDRAAQWLERTGLLEFANRTAGTLAYGQQRRLEIARCMVTQPRLLMLDEPAAGL 185 Query: 165 APLVVKQIFQAVKDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLAN 224 P + + ++ E +T+ ++E + + ++ V+ G +GT ++ + Sbjct: 186 NPRETVDLQALIAELRSEHGLTILLIEHDMKLVMGISDHVVVINQGCPLAAGTPEQVCRD 245 Query: 225 EEVRSAYL 232 EV AYL Sbjct: 246 PEVIKAYL 253 Lambda K H 0.320 0.136 0.377 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: 136 Number of extensions: 7 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: 236 Length of database: 256 Length adjustment: 24 Effective length of query: 212 Effective length of database: 232 Effective search space: 49184 Effective search space used: 49184 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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