Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate CCNA_03383 CCNA_03383 multidrug/protein/lipid ABC transporter family, ATP-binding and permease protein
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__Caulo:CCNA_03383 Length = 617 Score = 75.9 bits (185), Expect = 2e-18 Identities = 69/217 (31%), Positives = 108/217 (49%), Gaps = 14/217 (6%) Query: 14 AYGG---IQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHIEYLGQP 70 AY G + A+ G DL V GE V L+G +GAGK+T L+ + G I G Sbjct: 382 AYPGRPDLPALNGFDLRVKPGETVALVGPSGAGKSTVLRLLLRFYDPQ--SGCILLDGVN 439 Query: 71 LKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAY-TSDDKGQIAADIDKWFAVFPR 129 L+ + E V+ ++A+V + +F+ S +N+ G +D++ + AAD + Sbjct: 440 LRDAEPAE-VRARMALVAQDSPLFSG-SAMDNIRFGRPDATDEQVRAAADAAQATGFLSA 497 Query: 130 LKER----AAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIRN 185 L E + A TLSGG++Q LA+ARAL+ +LLLDE + L E++ + Sbjct: 498 LPEGFDTPVGERAKTLSGGQRQRLAIARALVREAPILLLDEATSALD-AESEQLVQQALA 556 Query: 186 VSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQG 222 + +G T L++ L+ A R VME G + QG Sbjct: 557 TAMEGRTTLVIAHRLATVLK-ADRIVVMEEGRVVEQG 592 Lambda K H 0.317 0.134 0.365 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: 299 Number of extensions: 11 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: 241 Length of database: 617 Length adjustment: 30 Effective length of query: 211 Effective length of database: 587 Effective search space: 123857 Effective search space used: 123857 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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