Align Uncharacterized protein (characterized, see rationale)
to candidate AZOBR_RS25115 AZOBR_RS25115 Fe-S oxidoreductase
Query= uniprot:B2TBW0 (256 letters) >FitnessBrowser__azobra:AZOBR_RS25115 Length = 256 Score = 151 bits (381), Expect = 1e-41 Identities = 96/244 (39%), Positives = 130/244 (53%), Gaps = 15/244 (6%) Query: 12 VALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTERVF 71 V F C +D FYPE G+A +ELL+ G++V +PQ Q+CCGQP NSG EA R Sbjct: 18 VYFFGTCLVDLFYPEAGMAGMELLKAQGVRVVFPQGQSCCGQPAYNSGYREEALKVARAQ 77 Query: 72 ARNFAGYDYIVGPSASCIHHVREHLTAL--EQTDEVK--KVRANAYELVEFLHDVVGARE 127 F G IV PS SC + +H L + DE + +V + +EL +FL V+ + Sbjct: 78 LDYFPGDWPIVVPSGSCAGMMSKHWPDLFKGEPDEARARQVASRVWELTQFLVQVLKVK- 136 Query: 128 FPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPDECC 187 F P ++ H SC A R E +++ +P+ LL + +E V+ R ECC Sbjct: 137 FEDQGPPVKITWHASCHAQR---EMGVTD-------EPKALLRQLANVELVELQREKECC 186 Query: 188 GFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERMKADARFIHI 247 GFGGTF+V +S M DKV D N GA+ +VSGD CLM+ G E K R +HI Sbjct: 187 GFGGTFAVRHPEISAAMVGDKVADIENTGAKAVVSGDCGCLMNISGALEGGKKPVRGVHI 246 Query: 248 AQVL 251 AQ L Sbjct: 247 AQFL 250 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: 224 Number of extensions: 7 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: 256 Length of database: 256 Length adjustment: 24 Effective length of query: 232 Effective length of database: 232 Effective search space: 53824 Effective search space used: 53824 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