Align arginine ABC transporter, periplasmic arginine-binding protein ArtJ (characterized)
to candidate 8502446 DvMF_3152 extracellular solute-binding protein family 3 (RefSeq)
Query= CharProtDB::CH_002541 (243 letters) >FitnessBrowser__Miya:8502446 Length = 271 Score = 95.1 bits (235), Expect = 1e-24 Identities = 77/257 (29%), Positives = 120/257 (46%), Gaps = 21/257 (8%) Query: 1 MKKLVL--AALLASFTFGASAAEKIN---------FGVSATYPPFESIGANN-EIVGFDI 48 MK+LVL AL T + A KI GV + PF I + +IVGFDI Sbjct: 1 MKRLVLLAVALCVVLTGTMAHAGKIEDIKARGALVCGVKDSTVPFGYIDEQSKQIVGFDI 60 Query: 49 DLAKALCKQMQAECTFTNHAFDSLIPSLKFRKYDAVISGMDITPERSKQVSFTTPYYENS 108 D+ KA+ ++ + + IP L D V + M ER + F+ Y+ + Sbjct: 61 DICKAVADKLGVKLELKTVTSATRIPMLTQGSVDMVAATMTHKFERDDVIDFSITYFMDG 120 Query: 109 AVVIAKKDT-YKTFADLKGKRIGMENGTTHQKYIQDQHPEVKTVSYDSYQNAFIDLKNGR 167 ++ KK K+ ADLKGK++ G+T +K I+ PE VS+D Y AF+ LK G+ Sbjct: 121 QKLLVKKGGGVKSAADLKGKKVATAKGSTSEKNIKAAQPEATVVSFDEYPQAFLALKQGK 180 Query: 168 IDGVFGDTAVVNEWLKTNPQLGVATEKVTD---PQYFGTGLGIAVRPDNKALLEKLNNAL 224 + V D+ ++ ++P+ E V D P+ +G GL ++ + +N L Sbjct: 181 AEAVTTDSTILLGLRNSDPEPD-KWEIVGDYISPEPYGLGLA----ENDSKFRDLVNRTL 235 Query: 225 AAIKADGTYQKISDQWF 241 + G Y K+ D+WF Sbjct: 236 VDLWNSGEYVKLYDKWF 252 Lambda K H 0.317 0.133 0.384 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: 171 Number of extensions: 13 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: 243 Length of database: 271 Length adjustment: 24 Effective length of query: 219 Effective length of database: 247 Effective search space: 54093 Effective search space used: 54093 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: 47 (22.7 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