Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate 5210577 Shew_3005 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein (RefSeq)
Query= uniprot:Q8EGS5 (464 letters) >FitnessBrowser__PV4:5210577 Length = 462 Score = 838 bits (2165), Expect = 0.0 Identities = 402/454 (88%), Positives = 428/454 (94%) Query: 9 AMGSQVHAYKADIFCRDETRVDWHSKALWLLREKRDRAAGSLPEWEQLRQLGSEIKLHTL 68 A+ S VHA KADIFC+DE RVDWHSKALW+LREKRDRAA SLPEWEQLRQLGSE+KLHTL Sbjct: 7 ALNSGVHAKKADIFCQDEARVDWHSKALWVLREKRDRAAASLPEWEQLRQLGSEMKLHTL 66 Query: 69 TNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVHEILASHKVKKLVKSKSMLTEECHLN 128 T+L +YLETFE+NC ANGI VHWAKDGAEHN+IVH ILA H+VKKLVKSKSMLTEECHLN Sbjct: 67 THLGEYLETFEKNCQANGIVVHWAKDGAEHNQIVHNILAKHQVKKLVKSKSMLTEECHLN 126 Query: 129 PYLEQRGIEVIDTDLGERIIQLAKMPPSHIVVPAIHMKKEEVGDLFHDKLGTKAGESDPL 188 PYLE +GIEVIDTDLGERIIQLAK PPSHIVVPAIH+KKEEVGDLFHDKLGT+AG SDPL Sbjct: 127 PYLESKGIEVIDTDLGERIIQLAKQPPSHIVVPAIHLKKEEVGDLFHDKLGTEAGASDPL 186 Query: 189 YLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKLQLHSMGID 248 YLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKLQLHSMGID Sbjct: 187 YLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKLQLHSMGID 246 Query: 249 KVVPDIDSAAVLLRTLARNATGQPVTTYSAFYRGPQVDGEMHVIIVDNGRTEMMKDKILA 308 K+VPD+DSAA+LLRTLARNATGQP+TTYS+FYRGPQ GEMHVIIVDNGRT+M++DKILA Sbjct: 247 KIVPDLDSAAILLRTLARNATGQPITTYSSFYRGPQDGGEMHVIIVDNGRTDMLQDKILA 306 Query: 309 ESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGATHDNTNSIAWACTLCGSCTY 368 ESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGA D+T+SI WACTLCGSC+Y Sbjct: 307 ESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGAQADDTHSIPWACTLCGSCSY 366 Query: 369 VCPTKVPLDKIIHHHRRLKAEAGKLPYGKNAYMPLVGKFMASTTLLNCSMGAARTALRIL 428 VCPTKVPLDKIIHHHRRLKA+AGKLPYGK YMPLVG FMAS T+LNCSM ARTALRIL Sbjct: 367 VCPTKVPLDKIIHHHRRLKAKAGKLPYGKRNYMPLVGNFMASETMLNCSMSVARTALRIL 426 Query: 429 PGSLLKPFSGAWGKYRELPVAPNSSFEAWFKKHR 462 PGSLLKPFSGAWGKYRELPVAP SSFEAWF K+R Sbjct: 427 PGSLLKPFSGAWGKYRELPVAPKSSFEAWFNKNR 460 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: 789 Number of extensions: 11 Number of successful extensions: 3 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: 462 Length adjustment: 33 Effective length of query: 431 Effective length of database: 429 Effective search space: 184899 Effective search space used: 184899 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