Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate WP_029132645.1 A3GO_RS0106040 iron-sulfur cluster-binding protein
Query= uniprot:E4PLR6 (483 letters) >NCBI__GCF_000428045.1:WP_029132645.1 Length = 472 Score = 541 bits (1393), Expect = e-158 Identities = 268/460 (58%), Positives = 338/460 (73%), Gaps = 2/460 (0%) Query: 13 DFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKAGALSRLPD 72 +F R +EAL + QLR+NFR+AMD LM KR+NAFPD E LR LG++I+A AL++ P+ Sbjct: 6 EFDQRVQEALNNPQLRSNFRIAMDGLMEKRSNAFPDKSFMEELRVLGSKIRANALAKQPE 65 Query: 73 LLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEMEMNDYLAE 132 LLEQLE T NG++VHWAET+E+AN +V I+E ++++KGKSMVSEEMEMN +L Sbjct: 66 LLEQLEANCTRNGIQVHWAETIEQANRIVLEIMERHNATRMIKGKSMVSEEMEMNHFLEA 125 Query: 133 RGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGE-PETEDVNQLIQI 191 +G C+ESD+GEYI+QLD+E PSHII PAIHK+ ++++KLF K + P +ED+ + + Sbjct: 126 QGKSCIESDLGEYIIQLDHETPSHIIAPAIHKSKQEIAKLFKAKHPDIPYSEDIETMTRS 185 Query: 192 GRRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTGIEKVVPN 251 R+ LR KF EA++G+SGVNFA+AETGTL LVENEGNGRM TT PPVHIAVTGIEKV+ Sbjct: 186 ARQVLRSKFYEAEIGLSGVNFAVAETGTLCLVENEGNGRMCTTVPPVHIAVTGIEKVLEK 245 Query: 252 LRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNGRTGAFADAQM 311 L DV PL+ LLTRSA GQ I+TY N+IS PRKP E DGP+EVHLVLLDN R+ + D ++ Sbjct: 246 LSDVPPLLKLLTRSASGQHISTYFNMISSPRKPGERDGPKEVHLVLLDNQRSKIYEDDEL 305 Query: 312 RQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHPSASSLCG 371 +L CIRCGACMNHCPVYTR+GGH YG + PGPIG I P GLDK P+AS+LCG Sbjct: 306 FDSLRCIRCGACMNHCPVYTRIGGHAYGSLIPGPIGSCIEPQKFGLDKFGVLPTASTLCG 365 Query: 372 ACGEVCPVKIPIPELLQRLRQENVKNPEQPQQVKGGGAKYSRTERWIWRGWQMLNTRPAL 431 ACGEVCPVKIP+P+LL RLR E V++ + G G++ S E IW+ W + PA+ Sbjct: 366 ACGEVCPVKIPLPKLLHRLRYEQVRD-DHTGATNGQGSQRSGKEAMIWKLWSWAHANPAV 424 Query: 432 YRSFLWAATRFRALAPKKAGPWTENHSAPVPARRSLHDLA 471 YRS A+ FR P K GPWT +AP A +SLH LA Sbjct: 425 YRSGTRLASLFRGAIPNKIGPWTRVRTAPKIAPKSLHQLA 464 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: 644 Number of extensions: 18 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: 472 Length adjustment: 34 Effective length of query: 449 Effective length of database: 438 Effective search space: 196662 Effective search space used: 196662 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 24 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