Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate WP_086511825.1 BZY95_RS20930 iron-sulfur cluster-binding protein
Query= uniprot:E4PLR6 (483 letters) >NCBI__GCF_002151265.1:WP_086511825.1 Length = 489 Score = 539 bits (1388), Expect = e-158 Identities = 277/487 (56%), Positives = 340/487 (69%), Gaps = 13/487 (2%) Query: 7 VTELTP-DFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKAG 65 V TP +F +A +AL + Q+R NFR AMD LM KR + F D D E LRELG I+ Sbjct: 6 VQTFTPREFHRQAHDALGNPQIRANFRKAMDGLMAKRRDVFSDWD-LETLRELGANIRLR 64 Query: 66 ALSRLPDLLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEME 125 AL++LPDLLE+LE NG++VHWAE +EA ++ I + V+KGKSMVSEEM Sbjct: 65 ALAKLPDLLERLEANCQANGIQVHWAENGDEACRIIREICQRHGAKAVIKGKSMVSEEMH 124 Query: 126 MNDYLAERGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGEPETEDV 185 +N +L E G+E LESD+GEY+VQL+ + PSHIIMPAIH N ++S++ H + G T DV Sbjct: 125 LNAHLEEAGIEALESDLGEYLVQLNEQTPSHIIMPAIHLNTDEISEIMHTRTGTERTRDV 184 Query: 186 NQLIQIGRRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTGI 245 + + R LR +FM ADVG+SGVNFA+AETGTL LVENEGNGRM+T PPVHIAVTGI Sbjct: 185 DTMTAAARAQLRERFMAADVGISGVNFAVAETGTLCLVENEGNGRMTTAVPPVHIAVTGI 244 Query: 246 EKVVPNLRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNGRTGA 305 EKVV +LRDV PL +LLTRSA GQ +TTY N+IS PRK E DGP EVHLVL+D+GR+ Sbjct: 245 EKVVEHLRDVPPLYALLTRSATGQHVTTYFNMISSPRKLGEHDGPNEVHLVLVDSGRSNI 304 Query: 306 FADAQMRQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHPS 365 + D ++ TL CIRCGACMNHCPVYTRVGGHTYG YPGPIG I+ PHM GL+ D P+ Sbjct: 305 YQDDELLDTLRCIRCGACMNHCPVYTRVGGHTYGTTYPGPIGSILMPHMMGLEATKDLPT 364 Query: 366 ASSLCGACGEVCPVKIPIPELLQRLRQENVKNPEQPQQVKGGGAKYSRTERWIWRGWQML 425 ASSLCGACGEVCPVKIPIP+LL RLR+E V E V G G K ++ E W+G+Q L Sbjct: 365 ASSLCGACGEVCPVKIPIPDLLVRLRREAV--GEGRGNVPGAGVKRTKKEVAAWKGFQWL 422 Query: 426 NTRPALYRSFLWAATRFRALAPKKAGPWTENHSAPVPARRSLHDLAARH---------LD 476 T P +RS A + +AL P K GPWTE +AP PA+ SLH L +H D Sbjct: 423 ATHPGAWRSSTAIAGKLQALMPSKLGPWTEYRTAPKPAKVSLHALVKQHKAKRHQAGKSD 482 Query: 477 QNGGRPS 483 ++GG+ S Sbjct: 483 EDGGKRS 489 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: 657 Number of extensions: 27 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: 489 Length adjustment: 34 Effective length of query: 449 Effective length of database: 455 Effective search space: 204295 Effective search space used: 204295 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: 52 (24.6 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