Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate 8499630 DvMF_0396 iron-sulfur cluster binding protein (RefSeq)
Query= uniprot:E4PLR6 (483 letters) >FitnessBrowser__Miya:8499630 Length = 475 Score = 499 bits (1286), Expect = e-146 Identities = 256/463 (55%), Positives = 326/463 (70%), Gaps = 6/463 (1%) Query: 13 DFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKAGALSRLPD 72 DF EALAD QLR NF+ A+ LM KR PDA ERE +R+ K AL++LP+ Sbjct: 7 DFTANVTEALADRQLRANFKSALTGLMKKRVAVLPDAAERERMRDDAEAAKRKALAKLPE 66 Query: 73 LLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEMEMNDYLAE 132 LLE+LE+K TENG+ VHWAET EAN ++ I+ + +++VKGKSMVSEEM +N +L Sbjct: 67 LLERLERKCTENGIIVHWAETTAEANEIILDIMRSHDATRLVKGKSMVSEEMHLNHFLET 126 Query: 133 RGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKL-GEPETEDVNQLIQI 191 G+E LE+D+GE+I+QL++E PSHII+PA+HKN +QV ++F D L G P T+ V +L I Sbjct: 127 HGIEALETDLGEFIIQLNHEPPSHIIVPAVHKNRQQVGRIFADNLQGIPYTDVVEELNAI 186 Query: 192 GRRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTGIEKVVPN 251 R+TLR KF VG+SGVNFA+AETGTL+LVENEGNGRM TT PPVH+AV G+EKVV + Sbjct: 187 ARKTLREKFRTGHVGLSGVNFAVAETGTLVLVENEGNGRMCTTVPPVHVAVMGLEKVVES 246 Query: 252 LRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNGRTGAFADAQM 311 L D+ PL+ LLT SA GQ +TTYVN I+ PRK E DGP+E+HLV+LDNGR+ ADAQ+ Sbjct: 247 LSDLPPLLRLLTASATGQLVTTYVNCITSPRKDGERDGPKEIHLVILDNGRSRMLADAQL 306 Query: 312 RQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHPSASSLCG 371 R+TL CIRCG C+NHCPVY R+GGH YG VYPGPIGKI+TP + GL +ASSLC Sbjct: 307 RRTLQCIRCGTCLNHCPVYIRIGGHAYGSVYPGPIGKILTPQIDGLADKGVLATASSLCN 366 Query: 372 ACGEVCPVKIPIPELLQRLRQENVKNPEQPQQVKGGGAKYSRTERWIWRGWQMLNTRPAL 431 AC EVCPV+IPIP +++R+R E + + VKG GAK + E +W+GW++ PAL Sbjct: 367 ACEEVCPVRIPIPGIIRRMRTE-AYDEKGDGVVKGHGAKKNLLETLVWKGWELTYRIPAL 425 Query: 432 YRSFLWAATRFRALAPKKAGP---WTENHSAPVPARRSLHDLA 471 R + RF P GP WT +AP A +SLH LA Sbjct: 426 NRFVVSMLGRFGDKLP-NVGPLKAWTSVRTAPRFAPKSLHQLA 467 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: 615 Number of extensions: 29 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: 475 Length adjustment: 34 Effective length of query: 449 Effective length of database: 441 Effective search space: 198009 Effective search space used: 198009 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: 51 (24.3 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