Align Uncharacterized protein (characterized, see rationale)
to candidate AZOBR_RS01615 AZOBR_RS01615 Fe-S oxidoreductase
Query= uniprot:B2TBW0 (256 letters) >FitnessBrowser__azobra:AZOBR_RS01615 Length = 261 Score = 156 bits (395), Expect = 4e-43 Identities = 91/248 (36%), Positives = 130/248 (52%), Gaps = 16/248 (6%) Query: 11 KVALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTERV 70 +V LF+ C +D + P VG A ++LLE G V+ P QTCCGQP N+G A A R Sbjct: 9 RVGLFVTCLVDVYRPTVGFAAVKLLEDAGCTVEVPASQTCCGQPAFNAGDRATARDLARS 68 Query: 71 FARNFAGYDYIVGPSASCIHHVREHLTALEQTD-----EVKKVRANAYELVEFLHDVVGA 125 F G+D++V PS SC +R+H L D + + A +ELV FL DV+G Sbjct: 69 TIAAFEGFDHVVVPSGSCAGQIRKHYPELLADDPAWAARARHLSARTHELVSFLTDVLGV 128 Query: 126 REFPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPDE 185 + A + + H+SCS LR E + E +PR LL V+G+ + + Sbjct: 129 TD-TGARYDGTITYHDSCSGLR---ELGVKE-------QPRRLLAKVEGLTLNELPGAEV 177 Query: 186 CCGFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERMKADARFI 245 CCGFGGTF V +S RM + K D A+ +++GDM CL++ G +R + R Sbjct: 178 CCGFGGTFCVKYPDISNRMVEAKTADIAGTKADTLLAGDMGCLLNMAGKLKREGSAVRVR 237 Query: 246 HIAQVLNG 253 H+A+VL G Sbjct: 238 HVAEVLAG 245 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: 210 Number of extensions: 13 Number of successful extensions: 4 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: 261 Length adjustment: 24 Effective length of query: 232 Effective length of database: 237 Effective search space: 54984 Effective search space used: 54984 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: 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