Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate 8501132 DvMF_1868 protein of unknown function DUF162 (RefSeq)
Query= uniprot:Q8EGS5 (464 letters) >FitnessBrowser__Miya:8501132 Length = 716 Score = 240 bits (613), Expect = 1e-67 Identities = 140/388 (36%), Positives = 204/388 (52%), Gaps = 23/388 (5%) Query: 70 NLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVHEILASHKVKKLVKSKSMLTEECHLNP 129 N+ F+ G+KVH AKD AE N I+ I + KK+VKSKSM EE LN Sbjct: 64 NMDALYAQFKAEAKKRGVKVHMAKDAAEANEIIARIAKNSNCKKIVKSKSMTAEETLLNH 123 Query: 130 YLEQRGIEVIDTDLGERIIQLAKMPPSHIVVPAIHMKKEEVGDLFHDKLGTKAGESDPLY 189 LE+ G+EVI+TDLGE IIQL P+H+V+PAIH+ + +V DLF + K E D Sbjct: 124 RLEEDGLEVIETDLGEWIIQLRHEGPTHMVMPAIHLSRYQVADLFSEVTKQKQ-EVDIQR 182 Query: 190 LTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKLQLHSMGIDK 249 L + AR LR+ F +AD ++G N AIA+ G + + TNEGNA + LP++ + G+DK Sbjct: 183 LVKVARRELRQHFATADMGISGANFAIAESGTIGLVTNEGNARLVTTLPRVHVALCGLDK 242 Query: 250 VVPDIDSAAVLLRTLARNATGQPVTTYSAFYRG-------PQVDGEMHVIIVDNGRTEMM 302 + P ++ A LR L RNATGQ +T+Y + G EMH++ +DNGR + Sbjct: 243 LTPSLNDALKSLRVLPRNATGQAITSYVTWITGANECKAAADEKKEMHIVFLDNGRRALA 302 Query: 303 KDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVG---ATHDNTNSIAWA 359 +D + ++ ++C+RCG C N CPVYR GG+ + G IG+ + D ++ Sbjct: 303 QDPLFSQVMRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGKDKARNLVQN 362 Query: 360 CTLCGSCTYVCPTKVPLDKIIHHHRRLKAEAGKLPYGKNAYMPLVGKFMASTTLLNCSMG 419 C C SC +C + L ++I R +E P L+GK + + L + + Sbjct: 363 CINCESCKSICAGGIDLPRLIKEIRARLSEEDGAP----VEATLLGKVLKNRKLFHTLLR 418 Query: 420 AARTALRILPGSLLKPFSGAWGKYRELP 447 + A KP +G R LP Sbjct: 419 FGKFA--------QKPVTGGTPYLRHLP 438 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: 716 Number of extensions: 23 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: 716 Length adjustment: 36 Effective length of query: 428 Effective length of database: 680 Effective search space: 291040 Effective search space used: 291040 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: 53 (25.0 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