Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate WP_038216210.1 Q392_RS27395 malate/lactate/ureidoglycolate dehydrogenase
Query= curated2:Q07251 (349 letters) >NCBI__GCF_000745855.1:WP_038216210.1 Length = 378 Score = 237 bits (605), Expect = 3e-67 Identities = 154/372 (41%), Positives = 191/372 (51%), Gaps = 40/372 (10%) Query: 11 LARDILAAQQVPADIADDVAEHLVESDRCGYISHGLSILPNYRTALDGHSVNPQGRAKCV 70 +AR I AA A+ A VA +LV ++ G+ SHG+ ++P Y A+ + P AK Sbjct: 11 VARVIAAAGSAEAE-AQTVAANLVLANLSGHDSHGVGMVPRYVDAVQEGGLKPNTGAKVT 69 Query: 71 LDQGTLMVFDGDGGFGQHVGKSVMQAAIERVRQHGHCIVTLRRSHHLGRMGHYGEMAAAA 130 LD GTL+ DG G+GQ VG+ MQ IER QHG CI+T+ SHH+GR+GH+ EMA AA Sbjct: 70 LDIGTLLALDGQRGYGQVVGEQAMQMGIERALQHGSCILTVGNSHHMGRIGHFAEMAVAA 129 Query: 131 GFVLLSFTNVINRAPVVAPFGGRVARLTTNPLCF-----------AGPMPNGRPP----- 174 G V L F NV++R PVVAPFGG R TNP C AGP G P Sbjct: 130 GLVSLHFVNVLSR-PVVAPFGGGDGRFGTNPCCIGVPLKRQERSAAGPPQGGAAPPGGSD 188 Query: 175 -----------LVVDIATSAIAINKARVLAEKGEPAPEGSIIGADGNPTTDASTMF---- 219 V+D ATS +A K RV KGE PEG +I G PTTD + Sbjct: 189 PHAVGERGGEHFVLDFATSRVAQGKMRVAHNKGEQVPEGYLIDERGAPTTDPGVVVVPQA 248 Query: 220 GEHPGALLPFGGHKGYALGVVAELLAGVLSGGGTIQPDNPRGGVATNNLFAVLLNPALDL 279 G GAL+ FG HKGY + V ELL G LSGGGT N + VL++PA Sbjct: 249 GGLFGALMTFGEHKGYGMAVACELLGGALSGGGTWHRAPDAARTVLNGMLTVLIDPA--- 305 Query: 280 GLDWQSA---EVEAFVRYLHDTPPAPGVDRVQYPGEYE-AANRAQASDTLNINPAIWRNL 335 L Q A E AFV +L PP G + VQ GE E A A+ D + I+ A W L Sbjct: 306 RLGTQQAFEQEAAAFVDWLRQCPPGAGFEGVQIAGEPERRARAARGRDGIAIDDATWAEL 365 Query: 336 ERLAQSLNVAVP 347 + VA+P Sbjct: 366 HAAGAKVGVALP 377 Lambda K H 0.319 0.136 0.409 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: 396 Number of extensions: 31 Number of successful extensions: 7 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: 349 Length of database: 378 Length adjustment: 29 Effective length of query: 320 Effective length of database: 349 Effective search space: 111680 Effective search space used: 111680 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 (21.7 bits) S2: 49 (23.5 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