Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate AO353_05710 AO353_05710 (Fe-S)-binding protein
Query= uniprot:E4PLR6 (483 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05710 Length = 484 Score = 742 bits (1915), Expect = 0.0 Identities = 368/481 (76%), Positives = 406/481 (84%), Gaps = 1/481 (0%) Query: 2 SQRIPVTELTPDFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNR 61 S IP + DFR RA EAL D QLRNNFR AMDSLM KRA +F DA ERE LR LGN Sbjct: 4 STLIPTVAVEEDFRTRAHEALGDKQLRNNFRSAMDSLMAKRAASFSDAFEREHLRALGNA 63 Query: 62 IKAGALSRLPDLLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVS 121 I+A ALS+LPDLLEQLEQ LT NGV VHWAETV+EAN +V II A + QV+KGKSMVS Sbjct: 64 IRARALSKLPDLLEQLEQNLTRNGVTVHWAETVDEANGIVLSIIRAHEARQVIKGKSMVS 123 Query: 122 EEMEMNDYLAERGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGEPE 181 EEMEMN LAE+GVECLESDMGE+IVQLD+EKPSHIIMPAIHKNA QV+ LFHDKLG Sbjct: 124 EEMEMNHVLAEQGVECLESDMGEFIVQLDHEKPSHIIMPAIHKNAGQVASLFHDKLGVEY 183 Query: 182 TEDVNQLIQIGRRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIA 241 T+DV+QLIQIGR+ LR+KF EAD+GVSGVNFA+AETGTLLLVENEGNGRMSTT PPVHIA Sbjct: 184 TKDVDQLIQIGRKVLRQKFFEADIGVSGVNFAVAETGTLLLVENEGNGRMSTTVPPVHIA 243 Query: 242 VTGIEKVVPNLRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNG 301 VTGIEKVV NLRDVVPL+SLLTRSALGQPITTYVN+ISGPRK ELDGP+EVHLVLLDNG Sbjct: 244 VTGIEKVVENLRDVVPLLSLLTRSALGQPITTYVNMISGPRKAHELDGPQEVHLVLLDNG 303 Query: 302 RTGAFADAQMRQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVP 361 R+ AFAD+++RQTLNCIRCGACMNHCPVYTR+GGH YGEVYPGPIGKIITPH+ GL KVP Sbjct: 304 RSQAFADSELRQTLNCIRCGACMNHCPVYTRIGGHAYGEVYPGPIGKIITPHLVGLAKVP 363 Query: 362 DHPSASSLCGACGEVCPVKIPIPELLQRLRQENVKNPEQPQQV-KGGGAKYSRTERWIWR 420 DHPSASSLCGACGEVCPVKIPIP LL+RLR+ENVK P+ P QV +G G+KYSR ER+IW Sbjct: 364 DHPSASSLCGACGEVCPVKIPIPALLRRLREENVKAPDSPHQVMRGQGSKYSRKERFIWN 423 Query: 421 GWQMLNTRPALYRSFLWAATRFRALAPKKAGPWTENHSAPVPARRSLHDLAARHLDQNGG 480 W LN+ P LYR F + ATR RAL P GPWT+NHSAP PA RSLHD+A HL + G Sbjct: 424 AWAKLNSSPTLYRLFGFFATRLRALTPNNIGPWTQNHSAPKPAARSLHDMAREHLAKQGD 483 Query: 481 R 481 R Sbjct: 484 R 484 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: 723 Number of extensions: 26 Number of successful extensions: 4 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: 484 Length adjustment: 34 Effective length of query: 449 Effective length of database: 450 Effective search space: 202050 Effective search space used: 202050 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 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