Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate 8499630 DvMF_0396 iron-sulfur cluster binding protein (RefSeq)
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__Miya:8499630 Length = 475 Score = 283 bits (724), Expect = 1e-80 Identities = 155/389 (39%), Positives = 225/389 (57%), Gaps = 3/389 (0%) Query: 9 EYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADA-KDHAAKNMDT 67 ++ + E+L + LR R D E+ + + A+A K A + Sbjct: 7 DFTANVTEALADRQLRANFKSALTGLMKKRVAVLPDAAERERMRDDAEAAKRKALAKLPE 66 Query: 68 LYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLEE 127 L + + + + G+ VH A T AEANEII I R ++ + +K KSM +EE HLNH LE Sbjct: 67 LLERLERKCTENGIIVHWAETTAEANEIILDIMRSHDATRLVKGKSMVSEEMHLNHFLET 126 Query: 128 DNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVD-IQRLVKV 186 +E +ETDLGE+IIQ+ HE PSH+++PA+H +R QV +F++ + D ++ L + Sbjct: 127 HGIEALETDLGEFIIQLNHEPPSHIIVPAVHKNRQQVGRIFADNLQGIPYTDVVEELNAI 186 Query: 187 ARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPT 246 AR+ LR F T +G+SG NFAVAETGT+ LV NEGN R+ TT+P VHVA+ GL+K+V + Sbjct: 187 ARKTLREKFRTGHVGLSGVNFAVAETGTLVLVENEGNGRMCTTVPPVHVAVMGLEKVVES 246 Query: 247 LHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALAEDPL 306 L D L++L +ATGQ +T+YV I + + DG KE+H+V LDNGR + D Sbjct: 247 LSDLPPLLRLLTASATGQLVTTYVNCITSPRK-DGERDGPKEIHLVILDNGRSRMLADAQ 305 Query: 307 FSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINC 366 + L+C+RCG C N CPVY +GGH G +Y G IG ILT G L C Sbjct: 306 LRRTLQCIRCGTCLNHCPVYIRIGGHAYGSVYPGPIGKILTPQIDGLADKGVLATASSLC 365 Query: 367 ESCKHICAGGIDLPRLIKEIRARLNEEEG 395 +C+ +C I +P +I+ +R +E+G Sbjct: 366 NACEEVCPVRIPIPGIIRRMRTEAYDEKG 394 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: 755 Number of extensions: 34 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: 475 Length adjustment: 36 Effective length of query: 681 Effective length of database: 439 Effective search space: 298959 Effective search space used: 298959 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