Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate AZOBR_RS01620 AZOBR_RS01620 putative oxidoreductase subunit with NAD(P)-binding domain and ferridoxin-like domain
Query= uniprot:Q8EGS5 (464 letters) >FitnessBrowser__azobra:AZOBR_RS01620 Length = 478 Score = 288 bits (736), Expect = 4e-82 Identities = 164/442 (37%), Positives = 238/442 (53%), Gaps = 25/442 (5%) Query: 42 KRDRAAGSLPEWEQLRQLGSEIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRI 101 +R +AA LPE+E LR G ++K H L NL YLE FE + G VHW + E Sbjct: 35 RRKQAADRLPEFEDLRDQGRDLKNHVLANLDTYLEAFEGKVIEQGGHVHWCRTDQEARDA 94 Query: 102 VHEILASHKVKKLVKSKSMLTEECHLNPYLEQRGIEVIDTDLGERIIQLAKMPPSHIVVP 161 + I K + K KSM++EE +N YLE G+ I+TDLGE IIQL + PPSHI+ P Sbjct: 95 ILGICRKVGAKTVTKGKSMISEEIGINDYLEANGLTPIETDLGEYIIQLRREPPSHIIAP 154 Query: 162 AIHMKKEEVGDLF---HDKLGTKAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIAD 218 A H+ K +V F H L +P L AR LR +F AD +TG N+ +A+ Sbjct: 155 AFHLSKADVEGTFRQAHTDLPADRVLDEPKVLIAEARQVLRRKFQQADVGITGANIMVAE 214 Query: 219 KGAVVVCTNEGNADMGANLPKLQLHSMGIDKVVPDIDSAAVLLRTLARNATGQPVTTYSA 278 G+ V+ TNEGN D+ LP++ + IDKVVP ++ AA++LR LAR+ATGQ + Y+ Sbjct: 215 TGSTVIVTNEGNGDLTQILPRVHVVIATIDKVVPTLEDAALVLRLLARSATGQEASAYTT 274 Query: 279 FYRGPQVDG------EMHVIIVDNGRTEMMKDKILAESLKCIRCGGCLNTCPVYRRSGGY 332 F GP+ G E HV+++DNGR+ ++ + + L+CIRCG C+N CPVY GG+ Sbjct: 275 FSTGPRRPGDLDGPEEFHVVLLDNGRSALLGTE-FQDVLRCIRCGACMNHCPVYGSVGGH 333 Query: 333 SYNYTIPGPIGIAVGAT---HDNTNSIAWACTLCGSCTYVCPTKVPLDKIIHHHRRLKAE 389 +Y + PGPIG + + A T CG C VCP ++PL K++ H R + E Sbjct: 334 AYGWVYPGPIGSVMQPALLGVKEAGHLPNASTFCGRCEAVCPMRIPLPKMMRHWREKEFE 393 Query: 390 AGKLPYGKNAYMPLVGKFMASTTLLNCSMGAARTALRILPGSLLK--------PFSGAWG 441 P + L G F L + A R A+R L G+L + P + W Sbjct: 394 QNLQPAAMRRGLALWGWFARRPALYH---AATRMAVRAL-GALGRGKGRFASLPLAQGWT 449 Query: 442 KYRELPVAPNSSFEAWFKKHRS 463 ++R++P +F+ + + ++ Sbjct: 450 RHRDMPAPEGKTFQQMWAERKA 471 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: 546 Number of extensions: 33 Number of successful extensions: 7 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: 478 Length adjustment: 33 Effective length of query: 431 Effective length of database: 445 Effective search space: 191795 Effective search space used: 191795 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