Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate 208547 DVU3033 iron-sulfur cluster-binding protein
Query= uniprot:E4PLR6 (483 letters) >MicrobesOnline__882:208547 Length = 717 Score = 295 bits (756), Expect = 3e-84 Identities = 155/380 (40%), Positives = 225/380 (59%), Gaps = 2/380 (0%) Query: 13 DFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKAGALSRLPD 72 ++R +E+L + LRN + RANAF D DE+ + E+ + K A + Sbjct: 9 EYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADA-KDHAAKNMDT 67 Query: 73 LLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEMEMNDYLAE 132 L Q + + + GVKVH A T EAN ++ I + +K KSM +EE +N L E Sbjct: 68 LYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLEE 127 Query: 133 RGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGEPETEDVNQLIQIG 192 VE +E+D+GE+I+Q+ +E PSH++MPAIH + QV+ LF + + + D+ +L+++ Sbjct: 128 DNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDIQRLVKVA 187 Query: 193 RRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTGIEKVVPNL 252 RR LR F AD+G+SG NFA+AETGT+ LV NEGN R+ TT P VH+A+ G++K+VP L Sbjct: 188 RRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPTL 247 Query: 253 RDVVPLVSLLTRSALGQPITTYVNLISGPRKPDE-LDGPEEVHLVLLDNGRTGAFADAQM 311 D + + +L R+A GQ IT+YV I G + + +DG +E+H+V LDNGR D Sbjct: 248 HDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALAEDPLF 307 Query: 312 RQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHPSASSLCG 371 Q L C+RCGAC N CPVY VGGH G +Y G IG I+T G DK + C Sbjct: 308 SQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINCE 367 Query: 372 ACGEVCPVKIPIPELLQRLR 391 +C +C I +P L++ +R Sbjct: 368 SCKHICAGGIDLPRLIKEIR 387 Lambda K H 0.317 0.135 0.403 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: 792 Number of extensions: 39 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: 483 Length of database: 717 Length adjustment: 37 Effective length of query: 446 Effective length of database: 680 Effective search space: 303280 Effective search space used: 303280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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