Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate 208547 DVU3033 iron-sulfur cluster-binding protein
Query= uniprot:Q8EGS5 (464 letters) >MicrobesOnline__882:208547 Length = 717 Score = 246 bits (627), Expect = 2e-69 Identities = 146/398 (36%), Positives = 213/398 (53%), Gaps = 25/398 (6%) Query: 61 SEIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVHEILASHKVKKLVKSKSM 120 ++ K H N+ F+ G+KVH A+ AE N I+ I + KK +KSKSM Sbjct: 55 ADAKDHAAKNMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSM 114 Query: 121 LTEECHLNPYLEQRGIEVIDTDLGERIIQLAKMPPSHIVVPAIHMKKEEVGDLFHDKLGT 180 EE HLN LE+ +EVI+TDLGE IIQ+ PSH+V+PAIH+ + +V DLF + Sbjct: 115 TAEETHLNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQ 174 Query: 181 KAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKL 240 K E D L + AR LR F +AD ++G N A+A+ G + + TNEGNA + LP++ Sbjct: 175 KQ-EVDIQRLVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRV 233 Query: 241 QLHSMGIDKVVPDIDSAAVLLRTLARNATGQPVTTYSAFYRGPQ-----VDG--EMHVII 293 + G+DK+VP + A L+ L RNATGQ +T+Y + G VDG EMH++ Sbjct: 234 HVALAGLDKLVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVF 293 Query: 294 VDNGRTEMMKDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVG---ATH 350 +DNGR + +D + ++ L+C+RCG C N CPVYR GG+ + G IG+ + Sbjct: 294 LDNGRRALAEDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGR 353 Query: 351 DNTNSIAWACTLCGSCTYVCPTKVPLDKIIHHHR-RLKAEAGKLPYGKNAYMPLVGKFMA 409 D ++ C C SC ++C + L ++I R RL E G +P L+GK + Sbjct: 354 DKARNLVQNCINCESCKHICAGGIDLPRLIKEIRARLNEEEG-MP----VETTLMGKMLK 408 Query: 410 STTLLNCSMGAARTALRILPGSLLKPFSGAWGKYRELP 447 + L + + A+ A KP +G R LP Sbjct: 409 NRKLFHTLLRFAKWA--------QKPVTGGTPYIRHLP 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: 761 Number of extensions: 28 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: 717 Length adjustment: 36 Effective length of query: 428 Effective length of database: 681 Effective search space: 291468 Effective search space used: 291468 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