Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate Dsui_1583 Dsui_1583 (4Fe-4S) cluster-containing protein
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__PS:Dsui_1583 Length = 470 Score = 316 bits (809), Expect = 2e-90 Identities = 192/462 (41%), Positives = 264/462 (57%), Gaps = 17/462 (3%) Query: 9 EYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVA-DAKDHAAKNMDT 67 +++ +E+L N L+ A+ V + RA A + + + + D ++ A +N+D Sbjct: 7 DFKARAREALANPNLQKALKLVQVKFVPGRAAAAAEFGDFETLRDAGRDIRNRALENLDL 66 Query: 68 LYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLEE 127 +F+ EA +RG +VH AR AAEAN II IA+ N KK +KSKSM +EE LN LE Sbjct: 67 WLERFEQEATRRGAQVHWARDAAEANAIIVGIAQANGVKKVVKSKSMVSEECGLNDALEA 126 Query: 128 DNVEVIETDLGEWIIQMR-HEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDIQRLVKV 186 V +ETDLGE+I+Q+ HE PSH+V P IH +R +V+DLF + + DI L + Sbjct: 127 AGVTPVETDLGEYILQINDHEPPSHIVAPVIHKTRDEVSDLFHAKHGKPRTEDIGALCRE 186 Query: 187 ARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPT 246 AR LR HF +ADMGISGANF VAETG+ +VTNEGN RL TT+PR+HVAL G++K+VPT Sbjct: 187 AREILRPHFLSADMGISGANFLVAETGSTVIVTNEGNGRLCTTVPRIHVALTGIEKVVPT 246 Query: 247 LHDALRSLKVLPRNATGQAITSYV---TWIGGANECEACVDGRKEMHIVFLDNGRRALAE 303 L D L++LPR+ATGQ IT+YV T + G+ + DG ++ HIV LDNGR + Sbjct: 247 LEDLSVLLRLLPRSATGQPITNYVSMNTGVAGSGDS----DGPEQFHIVLLDNGRSRVLG 302 Query: 304 DPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNC 363 L ++LRC+RCGAC N CPVY+ VGGH G +Y G +G +LT + G + A L Sbjct: 303 SEL-KEMLRCIRCGACMNHCPVYQAVGGHAYGWVYPGPMGSVLTPSYAGMEHAHELPHTA 361 Query: 364 INCESCKHICAGGIDLPRLIKEIRARLNEEEGM-----PVETTLMGKMLKNRKLFHTLLR 418 C C +C I LP L+++ R + E G+ + L G L+ Sbjct: 362 TGCGQCSAVCPVRIPLPELMRKER-EMQVEAGLRPWQERLSLKLWGWSASQSWLYGIGTA 420 Query: 419 FAKWAQKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRD 460 A K + G I LP G + PA A K FR+ Sbjct: 421 IAARFLKRLGGADQLIHRLPLGGGWTDG-RDFPAPAGKTFRE 461 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: 738 Number of extensions: 35 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: 470 Length adjustment: 36 Effective length of query: 681 Effective length of database: 434 Effective search space: 295554 Effective search space used: 295554 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