Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate 8501132 DvMF_1868 protein of unknown function DUF162 (RefSeq)
Query= uniprot:E4PLR6 (483 letters) >FitnessBrowser__Miya:8501132 Length = 716 Score = 284 bits (726), Expect = 8e-81 Identities = 153/371 (41%), Positives = 222/371 (59%), Gaps = 7/371 (1%) Query: 27 LRNNF-RVAMDSLMT----KRANAFPDADEREGLRELGNRIKAGALSRLPDLLEQLEQKL 81 L N F R AMD T RANAF DE+ + E+ + K A + L Q + + Sbjct: 18 LDNEFLREAMDKFATAYPVSRANAFRGLDEKAMIAEVADA-KDAAAKNMDALYAQFKAEA 76 Query: 82 TENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEMEMNDYLAERGVECLESD 141 + GVKVH A+ EAN ++ I + ++VK KSM +EE +N L E G+E +E+D Sbjct: 77 KKRGVKVHMAKDAAEANEIIARIAKNSNCKKIVKSKSMTAEETLLNHRLEEDGLEVIETD 136 Query: 142 MGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGEPETEDVNQLIQIGRRTLRRKFM 201 +GE+I+QL +E P+H++MPAIH + QV+ LF + + + D+ +L+++ RR LR+ F Sbjct: 137 LGEWIIQLRHEGPTHMVMPAIHLSRYQVADLFSEVTKQKQEVDIQRLVKVARRELRQHFA 196 Query: 202 EADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTGIEKVVPNLRDVVPLVSL 261 AD+G+SG NFAIAE+GT+ LV NEGN R+ TT P VH+A+ G++K+ P+L D + + + Sbjct: 197 TADMGISGANFAIAESGTIGLVTNEGNARLVTTLPRVHVALCGLDKLTPSLNDALKSLRV 256 Query: 262 LTRSALGQPITTYVNLISGPRK-PDELDGPEEVHLVLLDNGRTGAFADAQMRQTLNCIRC 320 L R+A GQ IT+YV I+G + D +E+H+V LDNGR D Q + C+RC Sbjct: 257 LPRNATGQAITSYVTWITGANECKAAADEKKEMHIVFLDNGRRALAQDPLFSQVMRCVRC 316 Query: 321 GACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHPSASSLCGACGEVCPVK 380 GAC N CPVY VGGH G +Y G IG I+T G DK + C +C +C Sbjct: 317 GACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGKDKARNLVQNCINCESCKSICAGG 376 Query: 381 IPIPELLQRLR 391 I +P L++ +R Sbjct: 377 IDLPRLIKEIR 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: 762 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 483 Length of database: 716 Length adjustment: 37 Effective length of query: 446 Effective length of database: 679 Effective search space: 302834 Effective search space used: 302834 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