Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate Pf1N1B4_1188 Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1188 Length = 484 Score = 286 bits (732), Expect = 2e-81 Identities = 152/381 (39%), Positives = 223/381 (58%), Gaps = 2/381 (0%) Query: 8 KEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADA-KDHAAKNMD 66 +++R ++L + LRN + + RA +F D E+ + + +A + A + Sbjct: 14 EDFRARAHKALADTQLRNNFRSAMDSLMSKRAASFSDAFEREHLRVLGNAVRARALSKLP 73 Query: 67 TLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLE 126 L Q + + GV VH A T EAN I+ I R + ++ IK KSM +EE +NH L Sbjct: 74 DLLEQLEQNLTRNGVTVHWAETVDEANGIVLSIIRAHEARQVIKGKSMVSEEMEMNHVLA 133 Query: 127 EDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDIQRLVKV 186 +E +E+D+GE+I+Q+ HE PSH++MPAIH + QVA LF + + D+ +L+++ Sbjct: 134 AQGIECLESDMGEFIVQLDHEKPSHIIMPAIHKNAGQVASLFHDKLGVEYTKDVDQLIQI 193 Query: 187 ARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPT 246 R+ LR F AD+G+SG NFAVAETGT+ LV NEGN R+ TT+P VH+A+ G++K+V Sbjct: 194 GRKVLRQKFFEADIGVSGVNFAVAETGTLLLVENEGNGRMSTTVPPVHIAVTGIEKVVEN 253 Query: 247 LHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALAEDPL 306 L D + L +L R+A GQ IT+YV I G + E +DG +E+H+V LDNGR D Sbjct: 254 LRDVVPLLSLLTRSALGQPITTYVNMISGPRK-EHELDGPQEVHLVLLDNGRSQAFADSE 312 Query: 307 FSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINC 366 Q L C+RCGAC N CPVY +GGH G +Y G IG I+T G K + C Sbjct: 313 LRQTLNCIRCGACMNHCPVYTRIGGHAYGEVYPGPIGKIITPHMVGLAKVPDHPSASSLC 372 Query: 367 ESCKHICAGGIDLPRLIKEIR 387 +C +C I +P L++ +R Sbjct: 373 GACGEVCPVKIPIPALLRRLR 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: 756 Number of extensions: 32 Number of successful extensions: 4 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: 484 Length adjustment: 37 Effective length of query: 680 Effective length of database: 447 Effective search space: 303960 Effective search space used: 303960 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