Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate RR42_RS21285 RR42_RS21285 (Fe-S)-binding protein
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__Cup4G11:RR42_RS21285 Length = 476 Score = 290 bits (741), Expect = 1e-82 Identities = 161/413 (38%), Positives = 232/413 (56%), Gaps = 3/413 (0%) Query: 9 EYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADA-KDHAAKNMDT 67 +++ + +LD+ LR++ +A RA F D DE + ++ +A + HA + Sbjct: 8 DFKARSRAALDDPKLRSSFRGAMDFLQAKRAVQFPDGDELEQLRDLGEAIRQHALSQLPD 67 Query: 68 LYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLEE 127 L Q + + GV+VH A TA EAN I+ IA+ + IK KSM +EE LNH L E Sbjct: 68 LLVQLEDKLTAAGVQVHWAETADEANAIVHGIAQARQASRVIKGKSMASEEIELNHYLAE 127 Query: 128 DNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSE-VTKQKQEVDIQRLVKV 186 ++ IE+D+GE+I+Q+ E PSH+VMPAIH +R +A+LF + + D+ L++ Sbjct: 128 RGIDCIESDMGEYIVQLAGEKPSHIVMPAIHKTRGDIAELFEQHIPGTPYTEDVDELIQT 187 Query: 187 ARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPT 246 RR LR F AD+G+SG NFA A+TGT+ LV NEGN RL TT+P VH+A+ G++K+V Sbjct: 188 GRRALRQEFVNADIGLSGVNFAAADTGTLWLVENEGNGRLSTTVPDVHIAIMGMEKVVAR 247 Query: 247 LHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALAEDPL 306 L + +L R+ATGQAIT+Y I G DG +E+H+V LDNGR D Sbjct: 248 LEHIVPLASLLTRSATGQAITTYFNLISGPRRAGE-RDGPREVHLVLLDNGRSQAYADEQ 306 Query: 307 FSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINC 366 L+C+RCGAC N CPVY +GGH G Y G IG I++ G D +L C Sbjct: 307 LRATLQCIRCGACMNHCPVYTRIGGHAYGTTYPGPIGKIISPHLLGLDATADLATASSLC 366 Query: 367 ESCKHICAGGIDLPRLIKEIRARLNEEEGMPVETTLMGKMLKNRKLFHTLLRF 419 +C +C I +P+L+ +R N + V L G+ K + H + RF Sbjct: 367 GACGEVCPVRIPIPQLLIRLRTEANRDPSEQVAHPLRGQGTKFSRGEHLVWRF 419 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: 719 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: 476 Length adjustment: 36 Effective length of query: 681 Effective length of database: 440 Effective search space: 299640 Effective search space used: 299640 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