Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate RR42_RS07435 RR42_RS07435 (Fe-S)-binding protein
Query= uniprot:Q8EGS5 (464 letters) >FitnessBrowser__Cup4G11:RR42_RS07435 Length = 469 Score = 271 bits (692), Expect = 4e-77 Identities = 161/430 (37%), Positives = 243/430 (56%), Gaps = 23/430 (5%) Query: 52 EWEQLRQLGSEIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVHEILASHKV 111 +++ R+ E + L NL +L TFE+N G V +A+ A+ R+V EI H V Sbjct: 44 DFDATREALKERRDRALQNLDVWLATFEENATRRGATVLFAETTADAARLVAEIAQKHGV 103 Query: 112 KKLVKSKSMLTEECHLNPYLEQRGIEVIDTDLGERIIQLAKM-PPSHIVVPAIHMKKEEV 170 KK++KSKSM+TEE LN L + G++ I+TDLGE I+Q+ PPSHI+ P +H KEE+ Sbjct: 104 KKVIKSKSMVTEEMRLNQVLGEMGVQSIETDLGEYILQINDAEPPSHIIAPVVHKDKEEI 163 Query: 171 GDLFHDKLGTKAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGN 230 DLF K+ K +D +TR AR LR +FLSAD +TG N IA+ G+V V TNEGN Sbjct: 164 ADLF-AKVHHKPRLTDISEMTREAREVLRPEFLSADMGVTGGNFIIAETGSVAVVTNEGN 222 Query: 231 ADMGANLPKLQLHSMGIDKVVPDIDSAAVLLRTLARNATGQPVTTYSAFYRGPQVDGE-- 288 M +P++ + GI+KV+P ++ A ++R L R+ATGQ ++ Y + GP+ +GE Sbjct: 223 EGMCTVMPRVHVAVTGIEKVLPTLEDLATVMRLLPRSATGQAISNYFSLLTGPRAEGERD 282 Query: 289 ----MHVIIVDNGRTEMMKDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGI 344 M+ ++VD GR+ ++ + L+CIRCG C+N CPVY++ GG++Y + PGP+G Sbjct: 283 GPEHMYFVLVDGGRSGLIGGD-FQDMLRCIRCGACMNHCPVYQKIGGHAYGWVYPGPMGS 341 Query: 345 AVGATH---DNTNSIAWACTLCGSCTYVCPTKVPLDKIIHHHRRLKAEAGKLPYGKNAYM 401 + ++ N + A TLCG C VCP +PL ++ R + E G P+ + + Sbjct: 342 VLTPSYVGIANALDLPQAATLCGECNRVCPASIPLSDLLRKLREKQMERGLRPWQERLGL 401 Query: 402 PLVGKFMASTTLLNCSMGAARTALRILP--GSLLK-----PFSG-AWGKYRELPVAPNSS 453 + G F+A L A R R+L G K P +G W + R+LP + Sbjct: 402 QVWG-FVARRPGLYAF--ATRIGARLLARMGGSSKLIARLPMAGRGWTETRDLPAPSGRT 458 Query: 454 FEAWFKKHRS 463 F +K+ R+ Sbjct: 459 FRELYKERRA 468 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: 457 Number of extensions: 21 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 464 Length of database: 469 Length adjustment: 33 Effective length of query: 431 Effective length of database: 436 Effective search space: 187916 Effective search space used: 187916 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