Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate WP_012978521.1 AZL_RS32095 iron-sulfur cluster-binding protein
Query= uniprot:E4PLR6 (483 letters) >NCBI__GCF_000010725.1:WP_012978521.1 Length = 474 Score = 510 bits (1314), Expect = e-149 Identities = 263/464 (56%), Positives = 317/464 (68%), Gaps = 7/464 (1%) Query: 12 PDFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKAGALSRLP 71 PDF + ALAD +LR NFR AMD LM+KRA F D E G+R L ++ ALS+LP Sbjct: 6 PDFAAASRAALADPELRGNFRRAMDGLMSKRAAQFADTGEWTGVRALAAAVRLRALSKLP 65 Query: 72 DLLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEMEMNDYLA 131 +LLE+LE+ T NG+ VHWA T ++AN++ I+ VVKGKSMV+EEM +N L Sbjct: 66 ELLEKLEETCTRNGITVHWAATTDDANAIALDILHKANAKLVVKGKSMVTEEMHLNAVLE 125 Query: 132 ERGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGEPET-EDVNQLIQ 190 + G+E LESD+GEYIVQ+D PSHIIMPAIH N RQ++ LF KL + E+ ED L Sbjct: 126 QDGIEVLESDLGEYIVQMDGTMPSHIIMPAIHLNTRQIAHLFKRKLKDAESREDAAYLTD 185 Query: 191 IGRRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTGIEKVVP 250 + RR LR KF ADVG+SGVN A+AETGTL L+ENEGNGRM TT PPVHIA G+EKVV Sbjct: 186 LARRVLRAKFEAADVGMSGVNAAVAETGTLCLIENEGNGRMCTTVPPVHIAFMGLEKVVE 245 Query: 251 NLRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNGRTGAFADAQ 310 L DV P++SLL RSA GQPITTYVN+ISGPRK E DGP EVHLV+LDNGR+G +AD + Sbjct: 246 RLEDVPPVISLLPRSATGQPITTYVNMISGPRKDGEKDGPREVHLVILDNGRSGIYADPE 305 Query: 311 MRQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHPSASSLC 370 +R TL CIRCGACMNHCPVYT+VGGH Y YPGPIGKI+ P + GL K P A ++C Sbjct: 306 LRDTLRCIRCGACMNHCPVYTKVGGHAYEAPYPGPIGKILVPQIEGLAKRGAMPHACTMC 365 Query: 371 GACGEVCPVKIPIPELLQRLRQENVKNPEQPQQVKGGGAKYSRTERWIWRGWQMLNTRPA 430 AC E+CPVKIPI E++ RLR E V+ VK GGAK SRTE +W GW +N P Sbjct: 366 NACVEICPVKIPIVEIMGRLRVEAVR---PGGAVKDGGAKASRTESMVWSGWAAMNASPT 422 Query: 431 LYRSFLWAATRFRALAPKK---AGPWTENHSAPVPARRSLHDLA 471 YR A ++ AP WT + P A R+LHDLA Sbjct: 423 AYRLATAAMSKLGNAAPSSLPVLKEWTNVRTKPRFAGRTLHDLA 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: 645 Number of extensions: 22 Number of successful extensions: 6 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: 474 Length adjustment: 34 Effective length of query: 449 Effective length of database: 440 Effective search space: 197560 Effective search space used: 197560 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