Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate GFF2943 HP15_2887 iron-sulfur cluster binding protein
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__Marino:GFF2943 Length = 479 Score = 287 bits (734), Expect = 1e-81 Identities = 152/381 (39%), Positives = 221/381 (58%), Gaps = 1/381 (0%) Query: 7 LKEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADAKDHAAKNMD 66 +KE+ Q ++ + +R + R AF+ D + + A+ + A N+ Sbjct: 14 VKEFHPRAQAAIHDPKIRKNFRSAMDGLMSKRKTAFEGWDLETLRDLGANVRLRALANLP 73 Query: 67 TLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLE 126 L Q + + + G+KVH A EA I+ I + + K IK KSM +EE LNH LE Sbjct: 74 DLLEQLEKKLIENGIKVHWAVDGDEACRIVRDICKARDAKTVIKGKSMVSEEMELNHYLE 133 Query: 127 EDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDIQRLVKV 186 E +E +E+DLGE+I+Q+ E PSH++MPAIH + +++ L E T D++ L Sbjct: 134 EQGIEALESDLGEYIVQLADETPSHIIMPAIHKNTGEISQLLHEKTGTDLSNDVEYLTAS 193 Query: 187 ARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPT 246 AR +LR F AD+G+SG NFAVAETGT+ LV NEGN R+ TT+P+ H+A+ G++K+VP+ Sbjct: 194 ARLQLREKFMNADVGVSGVNFAVAETGTLCLVENEGNGRMTTTVPKCHIAVTGIEKVVPS 253 Query: 247 LHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALAEDPL 306 + D L +L R+ATGQ IT+Y I G + E +DG +E+H+V +DNGR ++ +D Sbjct: 254 MEDVSALLALLTRSATGQHITTYFNMISGPRKAEE-LDGPEEVHLVLVDNGRSSIYQDDE 312 Query: 307 FSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINC 366 LRC+RCGAC N CPVY VGGH G Y G IG IL G D+ R+L C Sbjct: 313 LLDTLRCIRCGACMNHCPVYTRVGGHAYGTTYPGPIGKILMPHLIGLDEGRHLPSASSLC 372 Query: 367 ESCKHICAGGIDLPRLIKEIR 387 +C +C I +P L+ +R Sbjct: 373 GACGEVCPVKIPIPDLLVRLR 393 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: 766 Number of extensions: 30 Number of successful extensions: 3 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