Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate AZOBR_RS01620 AZOBR_RS01620 putative oxidoreductase subunit with NAD(P)-binding domain and ferridoxin-like domain
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__azobra:AZOBR_RS01620 Length = 478 Score = 266 bits (681), Expect = 1e-75 Identities = 166/435 (38%), Positives = 230/435 (52%), Gaps = 16/435 (3%) Query: 36 ASRANAFKDIDEKAIIAEVADAKDHAAKNMDTLYAQFKAEAEKRGVKVHLARTAAEANEI 95 A R F+D+ ++ D K+H N+DT F+ + ++G VH RT EA + Sbjct: 40 ADRLPEFEDLRDQG-----RDLKNHVLANLDTYLEAFEGKVIEQGGHVHWCRTDQEARDA 94 Query: 96 IARIARDNNCKKAIKSKSMTAEETHLNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMP 155 I I R K K KSM +EE +N LE + + IETDLGE+IIQ+R E PSH++ P Sbjct: 95 ILGICRKVGAKTVTKGKSMISEEIGINDYLEANGLTPIETDLGEYIIQLRREPPSHIIAP 154 Query: 156 AIHLSRYQVADLF----SEVTKQKQEVDIQRLVKVARRELRTHFATADMGISGANFAVAE 211 A HLS+ V F +++ + + + L+ AR+ LR F AD+GI+GAN VAE Sbjct: 155 AFHLSKADVEGTFRQAHTDLPADRVLDEPKVLIAEARQVLRRKFQQADVGITGANIMVAE 214 Query: 212 TGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPTLHDALRSLKVLPRNATGQAITSYVT 271 TG+ +VTNEGN L LPRVHV +A +DK+VPTL DA L++L R+ATGQ ++Y T Sbjct: 215 TGSTVIVTNEGNGDLTQILPRVHVVIATIDKVVPTLEDAALVLRLLARSATGQEASAYTT 274 Query: 272 WIGGANECEACVDGRKEMHIVFLDNGRRALAEDPLFSQVLRCVRCGACANVCPVYRLVGG 331 + G +DG +E H+V LDNGR AL F VLRC+RCGAC N CPVY VGG Sbjct: 275 FSTGPRR-PGDLDGPEEFHVVLLDNGRSALLGTE-FQDVLRCIRCGACMNHCPVYGSVGG 332 Query: 332 HKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINCESCKHICAGGIDLPRLIKEIRARLN 391 H G +Y G IG ++ G +A +L C C+ +C I LP++++ R + Sbjct: 333 HAYGWVYPGPIGSVMQPALLGVKEAGHLPNASTFCGRCEAVCPMRIPLPKMMRHWREKEF 392 Query: 392 EEEGMPVE----TTLMGKMLKNRKLFHTLLRFAKWAQKPVTGGTPYIRHLPQIFAKDHGF 447 E+ P L G + L+H R A A + G LP Sbjct: 393 EQNLQPAAMRRGLALWGWFARRPALYHAATRMAVRALGALGRGKGRFASLPLAQGWTR-H 451 Query: 448 KALPAIADKPFRDEW 462 + +PA K F+ W Sbjct: 452 RDMPAPEGKTFQQMW 466 Lambda K H 0.321 0.135 0.402 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: 731 Number of extensions: 45 Number of successful extensions: 5 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: 717 Length of database: 478 Length adjustment: 37 Effective length of query: 680 Effective length of database: 441 Effective search space: 299880 Effective search space used: 299880 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 (21.9 bits) S2: 53 (25.0 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