Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate 207247 DVU1782 iron-sulfur cluster-binding protein
Query= uniprot:Q8EGS5 (464 letters) >MicrobesOnline__882:207247 Length = 475 Score = 287 bits (734), Expect = 6e-82 Identities = 155/356 (43%), Positives = 213/356 (59%), Gaps = 10/356 (2%) Query: 39 LREKRDRAAGSLPEWEQLRQLGSEIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEH 98 LR KR E +++R G K L L LE E C ANGI VHWA+ E Sbjct: 33 LRAKRLNVFSDAEELDRMRVQGEANKRRALAQLPALLEQLEHRCTANGIIVHWAETTDEA 92 Query: 99 NRIVHEILASHKVKKLVKSKSMLTEECHLNPYLEQRGIEVIDTDLGERIIQLAKMPPSHI 158 NRIV +I+ SH LVK KSM++EE HLN YLE+ GIE ++TDLGE IIQL PPSHI Sbjct: 93 NRIVLDIMRSHDATTLVKGKSMVSEEMHLNAYLERHGIEALETDLGEFIIQLNHEPPSHI 152 Query: 159 VVPAIHMKKEEVGDLFHDKLGTKAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIAD 218 +VPA+H +++V +FH+KLG + + L AR LRE+F +A ++GVN AIA+ Sbjct: 153 IVPAVHKNRQQVARIFHEKLG-EPYVDEVEKLNAIARRTLREKFRTAQVGLSGVNFAIAE 211 Query: 219 KGAVVVCTNEGNADMGANLPKLQLHSMGIDKVVPDIDSAAVLLRTLARNATGQPVTTYSA 278 G +++ NEGN M +P + + MG++KVV ++ LLR L +ATGQ VTTY Sbjct: 212 TGTLLLVENEGNGRMCTTVPPVHIALMGLEKVVERLEDVPPLLRLLTGSATGQLVTTYVN 271 Query: 279 FYRGPQVDG------EMHVIIVDNGRTEMMKDKILAESLKCIRCGGCLNTCPVYRRSGGY 332 P+ G E+H++I+DNGR+ M+ D L+ +L+CIRCG CLN CPVY R GG+ Sbjct: 272 CITSPRKPGEKDGPREVHLVILDNGRSRMLADPQLSRTLQCIRCGTCLNHCPVYVRIGGH 331 Query: 333 SYNYTIPGPIGIAVGATHD---NTNSIAWACTLCGSCTYVCPTKVPLDKIIHHHRR 385 +Y+ PGPIG + D +A A +LC +C VCP ++P+ ++ RR Sbjct: 332 AYDSVYPGPIGKILTPQIDGLARKGVLATASSLCNACEEVCPVRIPIPALLRRLRR 387 Lambda K H 0.320 0.134 0.413 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: 502 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: 464 Length of database: 475 Length adjustment: 33 Effective length of query: 431 Effective length of database: 442 Effective search space: 190502 Effective search space used: 190502 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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