Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate CA265_RS18400 CA265_RS18400 iron-sulfur cluster-binding protein
Query= uniprot:Q8EGS5 (464 letters) >FitnessBrowser__Pedo557:CA265_RS18400 Length = 461 Score = 277 bits (708), Expect = 6e-79 Identities = 156/431 (36%), Positives = 237/431 (54%), Gaps = 19/431 (4%) Query: 44 DRAAGSLPEWEQLRQLGSEIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVH 103 +R E ++ IK + NL ++L FE N G KV WA D E + + Sbjct: 36 ERGLSKFENLEASKKKAHVIKWRVMENLDKFLPEFESNFQRRGGKVIWANDAEEAQQEIL 95 Query: 104 EILASHKVKKLVKSKSMLTEECHLNPYLEQRGIEVIDTDLGERIIQLAKMPPSHIVVPAI 163 I+ + K ++KSKSM TEE HLN +LE+ IE +++DLGE I+QL P HIV PA+ Sbjct: 96 NIIKRNNGKTVIKSKSMTTEEIHLNDFLEKNNIESLESDLGEYIVQLLGQAPYHIVTPAM 155 Query: 164 HMKKEEVGDLFHDKLGTKAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAVV 223 H+ ++ LFHDK GT ++ P L + AR LR+++L+AD ++G N IAD G++ Sbjct: 156 HLSATDIAQLFHDKFGTPI-DATPPQLVQKARELLRDKYLNADIGISGGNFLIADTGSIA 214 Query: 224 VCTNEGNADMGANLPKLQLHSMGIDKVVPDIDSAAVLLRTLARNATGQPVTTYSAFYRGP 283 + NEGNA + PK+ + +GI+KV+P I + LA + TGQ +T Y+ GP Sbjct: 215 LTENEGNARLSTTFPKIHIAIVGIEKVIPSIADLDLFWPLLASHGTGQNLTVYNTILSGP 274 Query: 284 ----QVDG--EMHVIIVDNGRTEMMKDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNYT 337 + DG EM+VI++DNGRT ++ K + L CIRCG CLN CPVY+ GG++YN T Sbjct: 275 RQPNETDGPEEMYVILLDNGRTNLLAQKDQRQGLYCIRCGACLNACPVYKNIGGHTYNTT 334 Query: 338 IPGPIGIAVGATH----DNTNSIAWACTLCGSCTYVCPTKVPLDKIIHHHRRLKAEAGKL 393 GPIG +V H + +++A +LCG C+ VCP K+ + K++ +RR A + Sbjct: 335 YSGPIG-SVITPHLKGMEEFKHLSYASSLCGKCSEVCPVKIDIHKMLLLNRRDAAAGHEN 393 Query: 394 PYGKNAYMPLVGKFMASTTLLNCSMGAARTALRILPGSLLKPFSGAWGKYRELPVAPNSS 453 + + + M ++ G + + L + F +WGKYRE+P + S Sbjct: 394 GKKEEIGWSMFSRMMQKRKWMDFFGGKFKNFM------LKRFFKKSWGKYREMPKVADKS 447 Query: 454 F-EAWFKKHRS 463 F + W + +S Sbjct: 448 FAKQWEEMKKS 458 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: 510 Number of extensions: 26 Number of successful extensions: 6 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: 461 Length adjustment: 33 Effective length of query: 431 Effective length of database: 428 Effective search space: 184468 Effective search space used: 184468 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