Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::A3ZI83 (242 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 139 bits (350), Expect = 7e-38 Identities = 78/237 (32%), Positives = 128/237 (54%), Gaps = 4/237 (1%) Query: 2 IELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVVN 61 + ++ ++ Y VL+ +NL++ +GE ++GPSG GK+T +R + GL+++S+G + +N Sbjct: 4 LSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSIAIN 63 Query: 62 NLVLNHKNKIEICRKYC-AMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKYL 120 ++ K M+FQ + L+PH+TV N+ +L K+S+ E + Sbjct: 64 GKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGVRQLDKQSRSVRLEEMLSLV 123 Query: 121 KVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMKE 180 K+ GL + YP LSGGQQQRV+IAR+L + +L DEP S +D + + ++ ++ Sbjct: 124 KLEGLGKR---YPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEIRA 180 Query: 181 ISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLG 237 I N + V VTH A AD + E G IV+ IP + +P T FLG Sbjct: 181 ILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLG 237 Lambda K H 0.317 0.133 0.372 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: 147 Number of extensions: 6 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: 242 Length of database: 341 Length adjustment: 26 Effective length of query: 216 Effective length of database: 315 Effective search space: 68040 Effective search space used: 68040 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 (21.7 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