Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate Dsui_0126 Dsui_0126 (4Fe-4S) cluster-containing protein
Query= uniprot:Q8EGS5 (464 letters) >FitnessBrowser__PS:Dsui_0126 Length = 479 Score = 311 bits (796), Expect = 4e-89 Identities = 169/433 (39%), Positives = 247/433 (57%), Gaps = 17/433 (3%) Query: 46 AAGSLPEWEQLRQLGSEIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVHEI 105 + G ++E LR +G+EI+ LT+L +LE FE A G V WA+DG E +++ +I Sbjct: 45 SVGQAGDFETLRGIGAEIRDTALTDLDAWLEAFEAKATATGATVLWARDGREAQQLIVDI 104 Query: 106 LASHKVKKLVKSKSMLTEECHLNPYLEQRGIEVIDTDLGERIIQLAKMPPSHIVVPAIHM 165 H VKK++KSKSML+EE LN LE G++ ++TDLGE I+QLAK PPSHI+ PAIH Sbjct: 105 AKRHGVKKVIKSKSMLSEEAGLNEGLEAAGVQSVETDLGEYILQLAKEPPSHILAPAIHK 164 Query: 166 KKEEVGDLF---HDKLGTKAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAV 222 KEEV +LF H + T G+ D LTR AR LRE FLSAD +TG N +A+ G+V Sbjct: 165 NKEEVDELFARCHGRPVTPEGQIDIPALTREARVALREHFLSADMGITGGNFLVAETGSV 224 Query: 223 VVCTNEGNADMGANLPKLQLHSMGIDKVVPDIDSAAVLLRTLARNATGQPVTTYSAFYRG 282 + TNEGN M LP++ + +GI+KV+P ++ + LLR L R+ATGQ ++ Y + G Sbjct: 225 ALVTNEGNGRMVTTLPRVHVAVVGIEKVIPTLEDLSALLRLLTRSATGQTISNYVSLLTG 284 Query: 283 PQVDG------EMHVIIVDNGRTEMMKDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNY 336 P+ +G M+ +++DNGR ++ E L+CIRCG C+N CPVY+ GG++Y + Sbjct: 285 PRAEGAVEGPEHMYFVLMDNGRAGLVGGD-FQEMLRCIRCGACMNHCPVYQSIGGHAYGW 343 Query: 337 TIPGPIGIAVGATH---DNTNSIAWACTLCGSCTYVCPTKVPLDKIIHHHRRLKAEAGKL 393 PGP+G + + + + A TLCG C+ VCP K+PL +++ R + E Sbjct: 344 VYPGPMGSVLTPLYTGLEQAPDLPQAATLCGQCSIVCPVKIPLPELLRKLREKQMETELR 403 Query: 394 PYGKNAYMPLVGKFMASTTLLNCSMGAARTALRILPGSLLK----PFSGAWGKYRELPVA 449 P+ + + G F A L + G AL++L G P W + R+ P Sbjct: 404 PWQERWALRTWGFFAARPRLYALAAGLGARALKLLAGGKASIRTLPGVPEWSRGRDFPAP 463 Query: 450 PNSSFEAWFKKHR 462 +F + R Sbjct: 464 QGKTFRELYAARR 476 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: 500 Number of extensions: 24 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