Align L-lactate dehydrogenase complex protein LldE (characterized, see rationale)
to candidate 6938322 Sama_2441 hypothetical protein (RefSeq)
Query= uniprot:Q8EGS4 (247 letters) >FitnessBrowser__SB2B:6938322 Length = 247 Score = 429 bits (1102), Expect = e-125 Identities = 204/247 (82%), Positives = 225/247 (91%) Query: 1 MKIALFIPCLVNQMMPDVAIATLELLEKLGHQVILPAGQTCCGQPMTNSGCFDAARSTTL 60 MKIALF PCLVNQMMP+VAIATL LLEKLGHQVI P GQTCCGQPMTNSGCF+ A++TTL Sbjct: 1 MKIALFTPCLVNQMMPEVAIATLSLLEKLGHQVIFPQGQTCCGQPMTNSGCFNEAKNTTL 60 Query: 61 KLLNAFKGVECDAIVCPAASCLVAAKENFHEFDNSPEAQAVINKLYELTEFLHDIAPIPA 120 KLLNAFKGVECDAIVCPAASCLVAAKENFHEFD SPEAQAVI+KLYELTEFLHD+AP+ Sbjct: 61 KLLNAFKGVECDAIVCPAASCLVAAKENFHEFDKSPEAQAVIDKLYELTEFLHDVAPVTQ 120 Query: 121 FNKPFAHKISLQLSCHGIRMLSLATPSEQMGPRFNKVEAVLANIAGIDIVYPDRRDECCG 180 FN+P A K+SLQLSCHGIRML LA PSE MGPR+NK+EA+L+ I G++I YP+R DECCG Sbjct: 121 FNRPVAKKLSLQLSCHGIRMLDLAAPSEYMGPRYNKMEALLSRIDGVEICYPERLDECCG 180 Query: 181 FGGTFAVDEGAVSAKMGKDKAQAHAATGAQYVVGFDPSCLLHLDGLIRRQQLPIEIRHIA 240 FGGTF+VDEGAVSAKMGKDKAQAHA TGA YVVGFDPSCL+HLDG IRR+QLPIE RH+A Sbjct: 181 FGGTFSVDEGAVSAKMGKDKAQAHANTGADYVVGFDPSCLMHLDGTIRRRQLPIETRHLA 240 Query: 241 QVLNAAL 247 Q+LN AL Sbjct: 241 QILNDAL 247 Lambda K H 0.324 0.137 0.416 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: 298 Number of extensions: 8 Number of successful extensions: 1 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: 247 Length of database: 247 Length adjustment: 24 Effective length of query: 223 Effective length of database: 223 Effective search space: 49729 Effective search space used: 49729 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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