Align Uncharacterized protein (characterized, see rationale)
to candidate AZOBR_RS25115 AZOBR_RS25115 Fe-S oxidoreductase
Query= uniprot:E4PLR5 (279 letters) >FitnessBrowser__azobra:AZOBR_RS25115 Length = 256 Score = 268 bits (685), Expect = 9e-77 Identities = 136/246 (55%), Positives = 173/246 (70%), Gaps = 2/246 (0%) Query: 27 EKPEAVTLFGTCVVDLFFPEAGLDTIRLLEREGVRVHFPQEQSCCGQPAWTSGYRDEAKA 86 E+PE+V FGTC+VDLF+PEAG+ + LL+ +GVRV FPQ QSCCGQPA+ SGYR+EA Sbjct: 13 ERPESVYFFGTCLVDLFYPEAGMAGMELLKAQGVRVVFPQGQSCCGQPAYNSGYREEALK 72 Query: 87 VARAQLDILDRSGLPVVVPSGSCAGMFRHHYPALFADEPDTLKRVEALAERTFELTEFLL 146 VARAQLD P+VVPSGSCAGM H+P LF EPD R +A R +ELT+FL+ Sbjct: 73 VARAQLDYFP-GDWPIVVPSGSCAGMMSKHWPDLFKGEPDEA-RARQVASRVWELTQFLV 130 Query: 147 KVCRVQLADRGAPSKIALHTSCSARREMNTHLHARELLQQLEGVERIDHDHESECCGFGG 206 +V +V+ D+G P KI H SC A+REM + LL+QL VE ++ E ECCGFGG Sbjct: 131 QVLKVKFEDQGPPVKITWHASCHAQREMGVTDEPKALLRQLANVELVELQREKECCGFGG 190 Query: 207 TFSVRMPEVSGAMVKDKTRSLIDSGAVEMVTADGGCLMNINGSLEKQKESFRGRHLASFL 266 TF+VR PE+S AMV DK + ++GA +V+ D GCLMNI+G+LE K+ RG H+A FL Sbjct: 191 TFAVRHPEISAAMVGDKVADIENTGAKAVVSGDCGCLMNISGALEGGKKPVRGVHIAQFL 250 Query: 267 WERTNG 272 ERT+G Sbjct: 251 KERTHG 256 Lambda K H 0.320 0.134 0.406 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: 280 Number of extensions: 7 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: 279 Length of database: 256 Length adjustment: 25 Effective length of query: 254 Effective length of database: 231 Effective search space: 58674 Effective search space used: 58674 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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