Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate GFF2943 HP15_2887 iron-sulfur cluster binding protein
Query= uniprot:Q8EGS5 (464 letters) >FitnessBrowser__Marino:GFF2943 Length = 479 Score = 307 bits (787), Expect = 4e-88 Identities = 170/416 (40%), Positives = 242/416 (58%), Gaps = 29/416 (6%) Query: 54 EQLRQLGSEIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVHEILASHKVKK 113 E LR LG+ ++L L NL LE E+ + NGIKVHWA DG E RIV +I + K Sbjct: 55 ETLRDLGANVRLRALANLPDLLEQLEKKLIENGIKVHWAVDGDEACRIVRDICKARDAKT 114 Query: 114 LVKSKSMLTEECHLNPYLEQRGIEVIDTDLGERIIQLAKMPPSHIVVPAIHMKKEEVGDL 173 ++K KSM++EE LN YLE++GIE +++DLGE I+QLA PSHI++PAIH E+ L Sbjct: 115 VIKGKSMVSEEMELNHYLEEQGIEALESDLGEYIVQLADETPSHIIMPAIHKNTGEISQL 174 Query: 174 FHDKLGTKAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADM 233 H+K GT +D YLT +AR LRE+F++AD ++GVN A+A+ G + + NEGN M Sbjct: 175 LHEKTGTDL-SNDVEYLTASARLQLREKFMNADVGVSGVNFAVAETGTLCLVENEGNGRM 233 Query: 234 GANLPKLQLHSMGIDKVVPDIDSAAVLLRTLARNATGQPVTTYSAFYRGP----QVDG-- 287 +PK + GI+KVVP ++ + LL L R+ATGQ +TTY GP ++DG Sbjct: 234 TTTVPKCHIAVTGIEKVVPSMEDVSALLALLTRSATGQHITTYFNMISGPRKAEELDGPE 293 Query: 288 EMHVIIVDNGRTEMMKDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVG 347 E+H+++VDNGR+ + +D L ++L+CIRCG C+N CPVY R GG++Y T PGPIG + Sbjct: 294 EVHLVLVDNGRSSIYQDDELLDTLRCIRCGACMNHCPVYTRVGGHAYGTTYPGPIG-KIL 352 Query: 348 ATH----DNTNSIAWACTLCGSCTYVCPTKVPLDKIIHHHRRLKAEAGKLPYGK------ 397 H D + A +LCG+C VCP K+P+ ++ R+ + KL K Sbjct: 353 MPHLIGLDEGRHLPSASSLCGACGEVCPVKIPIPDLLVRLRQESVDGDKLHPAKVRGHGA 412 Query: 398 --NAYMPLVGK----FMASTTLLNCSMGAARTALRILPGSLLKPFSGAWGKYRELP 447 ++ ++ K AS + GAA + P +GAW YR P Sbjct: 413 KRSSMEAMIWKGWAWMHASPGIYRFGTGAASKFRALQPSK-----AGAWTDYRTAP 463 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: 537 Number of extensions: 31 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: 479 Length adjustment: 33 Effective length of query: 431 Effective length of database: 446 Effective search space: 192226 Effective search space used: 192226 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