Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate Pf6N2E2_3383 Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF
Query= uniprot:E4PLR6 (483 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3383 Length = 242 Score = 397 bits (1020), Expect = e-115 Identities = 189/241 (78%), Positives = 207/241 (85%), Gaps = 1/241 (0%) Query: 242 VTGIEKVVPNLRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNG 301 VTGIEKVV NLRDVVPL+SLLTRSALGQPITTYVN+ISGPRK DELDGP+EVHLVLLDNG Sbjct: 1 VTGIEKVVENLRDVVPLLSLLTRSALGQPITTYVNMISGPRKADELDGPQEVHLVLLDNG 60 Query: 302 RTGAFADAQMRQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVP 361 R+ AFAD+++RQTLNCIRCGACMNHCPVYTR+GGH YGEVYPGPIGKIITPHM GL KVP Sbjct: 61 RSQAFADSELRQTLNCIRCGACMNHCPVYTRIGGHAYGEVYPGPIGKIITPHMVGLAKVP 120 Query: 362 DHPSASSLCGACGEVCPVKIPIPELLQRLRQENVKNPEQPQQV-KGGGAKYSRTERWIWR 420 DHPSASSLCGACGEVCPVKIPIP LL+RLR+ENVK P+ P QV +G G+KYS ER+IW Sbjct: 121 DHPSASSLCGACGEVCPVKIPIPALLRRLREENVKAPDSPHQVMRGQGSKYSPKERFIWN 180 Query: 421 GWQMLNTRPALYRSFLWAATRFRALAPKKAGPWTENHSAPVPARRSLHDLAARHLDQNGG 480 W LN+ P LYR F + ATR RAL P GPWT+NHSAP PA RSLHDLA HL+Q G Sbjct: 181 AWARLNSSPRLYRLFGFLATRLRALTPNNVGPWTQNHSAPKPAARSLHDLARDHLNQQGD 240 Query: 481 R 481 R Sbjct: 241 R 241 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: 385 Number of extensions: 16 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: 242 Length adjustment: 28 Effective length of query: 455 Effective length of database: 214 Effective search space: 97370 Effective search space used: 97370 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: 49 (23.5 bits)
Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate Pf6N2E2_3382 Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF
Query= uniprot:E4PLR6 (483 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3382 Length = 187 Score = 191 bits (484), Expect = 2e-53 Identities = 103/177 (58%), Positives = 118/177 (66%), Gaps = 17/177 (9%) Query: 5 IPVTELTPDFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKA 64 IP E+ DFR RA +AL D QLRNNFR AMDSLMTKRA +F DA ERE LR LGN ++A Sbjct: 7 IPTVEVQEDFRARAHKALDDTQLRNNFRSAMDSLMTKRATSFSDAHEREHLRVLGNAVRA 66 Query: 65 GALSRLPDLLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEM 124 ALS+LPDLLEQLE LT NGV VHWAETV+EAN +V II A + QV+KGKSMVSEEM Sbjct: 67 RALSKLPDLLEQLETNLTRNGVNVHWAETVDEANGIVLSIIRAHEARQVIKGKSMVSEEM 126 Query: 125 EMNDYLAERGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGEPE 181 EMN +L R +ECLESDMG IH+ AR H G+P+ Sbjct: 127 EMNHFLEARDIECLESDMG-----------------GIHRPARPREAFTHHYAGDPQ 166 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: 241 Number of extensions: 10 Number of successful extensions: 1 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: 187 Length adjustment: 26 Effective length of query: 457 Effective length of database: 161 Effective search space: 73577 Effective search space used: 73577 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: 48 (23.1 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