Align Uncharacterized protein (characterized, see rationale)
to candidate RR42_RS07430 RR42_RS07430 Fe-S oxidoreductase
Query= uniprot:B2TBW0 (256 letters) >FitnessBrowser__Cup4G11:RR42_RS07430 Length = 241 Score = 155 bits (391), Expect = 9e-43 Identities = 91/250 (36%), Positives = 132/250 (52%), Gaps = 17/250 (6%) Query: 10 MKVALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTER 69 M+V LF C +D PE+G + L+LLE+ G +V P+ QTCCGQP NSG + G Sbjct: 1 MRVGLFATCLVDLMRPEIGFSVLKLLEKAGFEVMVPEAQTCCGQPAYNSGERTASRGLAE 60 Query: 70 VFARNFAGYDYIVGPSASCIHHVREHLTAL-----EQTDEVKKVRANAYELVEFLHDVVG 124 F R F +DY+V PS SC V H L E + +R+ +EL +FL +V Sbjct: 61 KFLREFEMFDYVVIPSGSCGGMVLHHYADLLGDDPELNGRYEGLRSRVFELTDFLVNVAK 120 Query: 125 AREFPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPD 184 EF ++F R+ H+SCS LR L S+PR LL + G++ + + Sbjct: 121 LGEFD-SKFTGRITYHDSCSGLREL----------GVKSQPRALLAQLPGVQLSEMKDCE 169 Query: 185 ECCGFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERM-KADAR 243 CCGFGGTFSV +S + +K + +GA+ +V GD+ C+++ +G R + Sbjct: 170 ACCGFGGTFSVKYGNISTAIVDEKCANIKASGADAVVLGDLGCMLNIEGRLRRTGDTRTQ 229 Query: 244 FIHIAQVLNG 253 +HIAQVL G Sbjct: 230 VLHIAQVLAG 239 Lambda K H 0.323 0.137 0.422 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: 190 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: 256 Length of database: 241 Length adjustment: 24 Effective length of query: 232 Effective length of database: 217 Effective search space: 50344 Effective search space used: 50344 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 46 (22.3 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