Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate WP_013552998.1 NITSA_RS00135 lactate utilization protein
Query= uniprot:Q8EGS5 (464 letters) >NCBI__GCF_000186245.1:WP_013552998.1 Length = 452 Score = 435 bits (1118), Expect = e-126 Identities = 223/451 (49%), Positives = 291/451 (64%), Gaps = 5/451 (1%) Query: 15 HAYKADIFCRDETRVDWHSKALWLLREKRDRAAGSLPEWEQLRQLGSEIKLHTLTNLAQY 74 H A+ F + R WH +ALW +R+KRDRA S+PEWE+LRQ +IK HTL +L Y Sbjct: 4 HPRNAEAFLANAERARWHDQALWFVRQKRDRAMHSVPEWEELRQAAEQIKAHTLEHLGHY 63 Query: 75 LETFEQNCLANGIKVHWAKDGAEHNRIVHEILASHKVKKLVKSKSMLTEECHLNPYLEQR 134 LE FE NGI+V+WA+D AE IV +L K++VKSKSMLTEEC LNP+LE + Sbjct: 64 LERFESQAQTNGIEVYWAEDAAEMREIVTRLLKEQGAKRVVKSKSMLTEECGLNPHLEAK 123 Query: 135 GIEVIDTDLGERIIQLAKMPPSHIVVPAIHMKKEEVGDLFHDKLGTKAGESDPLYLTRAA 194 GIEV DTDLGERI+QLAK PPSHIV+PAIH++KEEVG +F + LGT E+DP LTRAA Sbjct: 124 GIEVTDTDLGERIVQLAKQPPSHIVLPAIHLRKEEVGRIFAEHLGTDPSETDPERLTRAA 183 Query: 195 RAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKLQLHSMGIDKVVPDI 254 R HLR++FL ADAA+TGVN A+A++G +VVCTNEGNAD+G LP L + MG++KV+P Sbjct: 184 RTHLRQKFLKADAAITGVNFALAEEGGIVVCTNEGNADLGTALPDLHIACMGLEKVIPSA 243 Query: 255 DSAAVLLRTLARNATGQPVTTYSAFYRGPQVDGEMHVIIVDNGRTEMMKDKILAESLKCI 314 V R LAR+ATGQ VT Y++ + P+ G + V+IVDNGR+ ++ DK L CI Sbjct: 244 RELGVFTRLLARSATGQAVTAYTSHFLRPKEGGRLCVVIVDNGRSALL-DKKAEALLSCI 302 Query: 315 RCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGATHD--NTNSIAWACTLCGSCTYVCPT 372 RCG C+NTCPVYRRSGG+SY +PGPIG A+ D ++ +ACTLC SC VCP Sbjct: 303 RCGACMNTCPVYRRSGGHSYQSVVPGPIGSALAGERDPGEYATLPFACTLCASCDAVCPV 362 Query: 373 KVPLDKIIHHHRRLKAEAGKLPYGKNAYMPLVGKFMASTTLLNCSMGAARTALRILPGSL 432 ++ L ++ R + K + + F+A ++ AL+ LP L Sbjct: 363 RIDLHDRLYEEREACVQVPAFA-PKRRGLRIAAFFLARPKWRRAAVRGLGRALKYLPRRL 421 Query: 433 LKPFSGAWGKYRELP-VAPNSSFEAWFKKHR 462 + WG RELP AP S E + ++ R Sbjct: 422 IYNRFNTWGLDRELPRPAPKSFRELYEERQR 452 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: 565 Number of extensions: 22 Number of successful extensions: 5 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: 452 Length adjustment: 33 Effective length of query: 431 Effective length of database: 419 Effective search space: 180589 Effective search space used: 180589 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 24 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