Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate Dsui_0126 Dsui_0126 (4Fe-4S) cluster-containing protein
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__PS:Dsui_0126 Length = 479 Score = 303 bits (777), Expect = 1e-86 Identities = 181/468 (38%), Positives = 262/468 (55%), Gaps = 20/468 (4%) Query: 9 EYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEV-------ADAKDHA 61 ++R E L + L++ + + RA + D + A+ +D A Sbjct: 7 QFRARAAERLADPALQSKLGGAKQLFVGGRARVVAEFDSVGQAGDFETLRGIGAEIRDTA 66 Query: 62 AKNMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHL 121 ++D F+A+A G V AR EA ++I IA+ + KK IKSKSM +EE L Sbjct: 67 LTDLDAWLEAFEAKATATGATVLWARDGREAQQLIVDIAKRHGVKKVIKSKSMLSEEAGL 126 Query: 122 NHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSE-----VTKQKQ 176 N LE V+ +ETDLGE+I+Q+ E PSH++ PAIH ++ +V +LF+ VT + Q Sbjct: 127 NEGLEAAGVQSVETDLGEYILQLAKEPPSHILAPAIHKNKEEVDELFARCHGRPVTPEGQ 186 Query: 177 EVDIQRLVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVA 236 +DI L + AR LR HF +ADMGI+G NF VAETG++ LVTNEGN R+VTTLPRVHVA Sbjct: 187 -IDIPALTREARVALREHFLSADMGITGGNFLVAETGSVALVTNEGNGRMVTTLPRVHVA 245 Query: 237 LAGLDKLVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDN 296 + G++K++PTL D L++L R+ATGQ I++YV+ + G E V+G + M+ V +DN Sbjct: 246 VVGIEKVIPTLEDLSALLRLLTRSATGQTISNYVSLLTGP-RAEGAVEGPEHMYFVLMDN 304 Query: 297 GRRALAEDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKA 356 GR L F ++LRC+RCGAC N CPVY+ +GGH G +Y G +G +LT + G ++A Sbjct: 305 GRAGLVGGD-FQEMLRCIRCGACMNHCPVYQSIGGHAYGWVYPGPMGSVLTPLYTGLEQA 363 Query: 357 RNLVQNCINCESCKHICAGGIDLPRLIKEIRARLNEEEGMPVE----TTLMGKMLKNRKL 412 +L Q C C +C I LP L++++R + E E P + G +L Sbjct: 364 PDLPQAATLCGQCSIVCPVKIPLPELLRKLREKQMETELRPWQERWALRTWGFFAARPRL 423 Query: 413 FHTLLRFAKWAQKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRD 460 + A K + GG IR LP + G + PA K FR+ Sbjct: 424 YALAAGLGARALKLLAGGKASIRTLPGVPEWSRG-RDFPAPQGKTFRE 470 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: 791 Number of extensions: 38 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: 479 Length adjustment: 37 Effective length of query: 680 Effective length of database: 442 Effective search space: 300560 Effective search space used: 300560 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