Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate 207247 DVU1782 iron-sulfur cluster-binding protein
Query= uniprot:E4PLR6 (483 letters) >MicrobesOnline__882:207247 Length = 475 Score = 528 bits (1360), Expect = e-154 Identities = 268/461 (58%), Positives = 332/461 (72%), Gaps = 5/461 (1%) Query: 13 DFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKAGALSRLPD 72 DF+G ALAD QLR NFR A+D L KR N F DA+E + +R G K AL++LP Sbjct: 8 DFKGNVTGALADRQLRANFRSALDGLRAKRLNVFSDAEELDRMRVQGEANKRRALAQLPA 67 Query: 73 LLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEMEMNDYLAE 132 LLEQLE + T NG+ VHWAET +EAN +V I+ + + +VKGKSMVSEEM +N YL Sbjct: 68 LLEQLEHRCTANGIIVHWAETTDEANRIVLDIMRSHDATTLVKGKSMVSEEMHLNAYLER 127 Query: 133 RGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGEPETEDVNQLIQIG 192 G+E LE+D+GE+I+QL++E PSHII+PA+HKN +QV+++FH+KLGEP ++V +L I Sbjct: 128 HGIEALETDLGEFIIQLNHEPPSHIIVPAVHKNRQQVARIFHEKLGEPYVDEVEKLNAIA 187 Query: 193 RRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTGIEKVVPNL 252 RRTLR KF A VG+SGVNFAIAETGTLLLVENEGNGRM TT PPVHIA+ G+EKVV L Sbjct: 188 RRTLREKFRTAQVGLSGVNFAIAETGTLLLVENEGNGRMCTTVPPVHIALMGLEKVVERL 247 Query: 253 RDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNGRTGAFADAQMR 312 DV PL+ LLT SA GQ +TTYVN I+ PRKP E DGP EVHLV+LDNGR+ AD Q+ Sbjct: 248 EDVPPLLRLLTGSATGQLVTTYVNCITSPRKPGEKDGPREVHLVILDNGRSRMLADPQLS 307 Query: 313 QTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHPSASSLCGA 372 +TL CIRCG C+NHCPVY R+GGH Y VYPGPIGKI+TP + GL + +ASSLC A Sbjct: 308 RTLQCIRCGTCLNHCPVYVRIGGHAYDSVYPGPIGKILTPQIDGLARKGVLATASSLCNA 367 Query: 373 CGEVCPVKIPIPELLQRLRQENVKNPEQPQQVKGGGAKYSRTERWIWRGWQMLNTRPALY 432 C EVCPV+IPIP LL+RLR+E+ P + VKG G+K + E+ +W+GW+M+ + PALY Sbjct: 368 CEEVCPVRIPIPALLRRLRRESYAPPGE-GVVKGAGSKRTLFEKAVWKGWEMVYSHPALY 426 Query: 433 RSFLWAATRFRALAPKKAGP---WTENHSAPVPARRSLHDL 470 L RF P K GP WT +AP A SLH+L Sbjct: 427 SFVLKVLGRFGHRLP-KVGPLKAWTSVRTAPRFASTSLHEL 466 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: 614 Number of extensions: 31 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: 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