Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate 14445 b0307 predicted amino acid dehydrogenase with NAD(P)-binding domain and ferridoxin-like domain (NCBI)
Query= uniprot:Q8EGS5 (464 letters) >FitnessBrowser__Keio:14445 Length = 475 Score = 302 bits (773), Expect = 2e-86 Identities = 166/434 (38%), Positives = 247/434 (56%), Gaps = 15/434 (3%) Query: 43 RDRAAGSLPEWEQLRQLGSEIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIV 102 R + L WE+ R ++I+ H L+NL YL + NG V++A+ + R + Sbjct: 38 RQKMVDELGHWEEWRDRAAQIRDHVLSNLDAYLYQLSEKVTQNGGHVYFARTKEDATRYI 97 Query: 103 HEILASHKVKKLVKSKSMLTEECHLNPYLEQRGIEVIDTDLGERIIQLAKMPPSHIVVPA 162 ++ +K+VKSKSM+TEE +N L+ GI+VI+TDLGE I+QL + PPSH+VVPA Sbjct: 98 LQVAQRKNARKVVKSKSMVTEEIGVNHVLQDAGIQVIETDLGEYILQLDQDPPSHVVVPA 157 Query: 163 IHMKKEEVGDLFHDKLGTKAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAV 222 IH + ++ + H++LG + G P +T R +RE FLSA+ +TG N A+A+ G+V Sbjct: 158 IHKDRHQIRRVLHERLGYE-GPETPEAMTLFIRQKIREDFLSAEIGITGCNFAVAETGSV 216 Query: 223 VVCTNEGNADMGANLPKLQLHSMGIDKVVPDIDSAAVLLRTLARNATGQPVTTYSAFYRG 282 + TNEGNA M LPK + MG++++ P VL+ LAR+A G +T Y+ + G Sbjct: 217 CLVTNEGNARMCTTLPKTHIAVMGMERIAPTFAEVDVLITMLARSAVGARLTGYNTWLTG 276 Query: 283 PQ----VDG--EMHVIIVDNGRTEMMKDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNY 336 P+ VDG E H++IVDNGR+E++ + + L+CIRCG C+NTCP YR GG+ Y Sbjct: 277 PREAGHVDGPEEFHLVIVDNGRSEVLASE-FRDVLRCIRCGACMNTCPAYRHIGGHGYGS 335 Query: 337 TIPGPIGIAVG---ATHDNTNSIAWACTLCGSCTYVCPTKVPLDKIIHHHRRLKAEAGKL 393 PGPIG + + + + +AC+LC +C VCP ++PL K+I HRR+ AE G Sbjct: 336 IYPGPIGAVISPLLGGYKDFKDLPYACSLCTACDNVCPVRIPLSKLILRHRRVMAEKGIT 395 Query: 394 PYGKNAYMPLVGKFMASTTLLNCSMGA-ARTALRILPGSLLKPFSGA---WGKYRELPVA 449 + + + + L M A A A + G GA W + R+LP A Sbjct: 396 AKAEQRAIKMFAYANSHPGLWKVGMMAGAHAASWFINGGKTPLKFGAISDWMEARDLPEA 455 Query: 450 PNSSFEAWFKKHRS 463 SF +WFKKH++ Sbjct: 456 DGESFRSWFKKHQA 469 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: 525 Number of extensions: 29 Number of successful extensions: 8 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: 475 Length adjustment: 33 Effective length of query: 431 Effective length of database: 442 Effective search space: 190502 Effective search space used: 190502 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