Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate Pf1N1B4_1188 Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF
Query= uniprot:E4PLR6 (483 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1188 Length = 484 Score = 741 bits (1912), Expect = 0.0 Identities = 365/478 (76%), Positives = 406/478 (84%), Gaps = 1/478 (0%) Query: 5 IPVTELTPDFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKA 64 IP + DFR RA +ALAD QLRNNFR AMDSLM+KRA +F DA ERE LR LGN ++A Sbjct: 7 IPTVAVEEDFRARAHKALADTQLRNNFRSAMDSLMSKRAASFSDAFEREHLRVLGNAVRA 66 Query: 65 GALSRLPDLLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEM 124 ALS+LPDLLEQLEQ LT NGV VHWAETV+EAN +V II A + QV+KGKSMVSEEM Sbjct: 67 RALSKLPDLLEQLEQNLTRNGVTVHWAETVDEANGIVLSIIRAHEARQVIKGKSMVSEEM 126 Query: 125 EMNDYLAERGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGEPETED 184 EMN LA +G+ECLESDMGE+IVQLD+EKPSHIIMPAIHKNA QV+ LFHDKLG T+D Sbjct: 127 EMNHVLAAQGIECLESDMGEFIVQLDHEKPSHIIMPAIHKNAGQVASLFHDKLGVEYTKD 186 Query: 185 VNQLIQIGRRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTG 244 V+QLIQIGR+ LR+KF EAD+GVSGVNFA+AETGTLLLVENEGNGRMSTT PPVHIAVTG Sbjct: 187 VDQLIQIGRKVLRQKFFEADIGVSGVNFAVAETGTLLLVENEGNGRMSTTVPPVHIAVTG 246 Query: 245 IEKVVPNLRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNGRTG 304 IEKVV NLRDVVPL+SLLTRSALGQPITTYVN+ISGPRK ELDGP+EVHLVLLDNGR+ Sbjct: 247 IEKVVENLRDVVPLLSLLTRSALGQPITTYVNMISGPRKEHELDGPQEVHLVLLDNGRSQ 306 Query: 305 AFADAQMRQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHP 364 AFAD+++RQTLNCIRCGACMNHCPVYTR+GGH YGEVYPGPIGKIITPHM GL KVPDHP Sbjct: 307 AFADSELRQTLNCIRCGACMNHCPVYTRIGGHAYGEVYPGPIGKIITPHMVGLAKVPDHP 366 Query: 365 SASSLCGACGEVCPVKIPIPELLQRLRQENVKNPEQPQQV-KGGGAKYSRTERWIWRGWQ 423 SASSLCGACGEVCPVKIPIP LL+RLR+ENVK P+ P QV +G G+KYSR ER+IW W Sbjct: 367 SASSLCGACGEVCPVKIPIPALLRRLREENVKAPDSPHQVMRGQGSKYSRKERFIWNAWA 426 Query: 424 MLNTRPALYRSFLWAATRFRALAPKKAGPWTENHSAPVPARRSLHDLAARHLDQNGGR 481 LN+ P LYR F + ATR RAL P GPWT+NHSAP PA RSLHD+A HL + G R Sbjct: 427 KLNSSPTLYRLFGFFATRLRALTPSNVGPWTQNHSAPKPAARSLHDMAREHLAKQGDR 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: 725 Number of extensions: 27 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