Align Short-chain dehydrogenase (characterized, see rationale)
to candidate RR42_RS24995 RR42_RS24995 hypothetical protein
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__Cup4G11:RR42_RS24995 Length = 259 Score = 115 bits (287), Expect = 1e-30 Identities = 86/250 (34%), Positives = 126/250 (50%), Gaps = 7/250 (2%) Query: 5 LQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQLEL 64 ++ K +IVTGGASGIG A + LAA GA+ + R LT RA + ++ Sbjct: 12 IEGKSIIVTGGASGIGEAAARLLAANGALLTIADRGSNGAALAKELTDQGLRAQFVETDI 71 Query: 65 QDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVGL--DAGRNEFVASLERNLIHYYV-MA 121 EA V VR +GRLD NNAGV ++ L + +F + N+I ++ M Sbjct: 72 SSEADVIAMVEAAVRSYGRLDRAFNNAGVPNAGKLLAELTEEDFRRCHDVNVIGTFLCMK 131 Query: 122 HYCVPHLKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNAL 181 H + LK GAI+N SS L + Y ASK A +T+ AA +RVNA+ Sbjct: 132 HEILAMLKTGGGAIVNCSSIHGLIYTARAAEYTASKHAITGMTKAAAADYGLQNIRVNAI 191 Query: 182 IPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTTG 241 P+ TP+Y ++ T + +E+++ + L R + E A A++LLS +S TG Sbjct: 192 APSSTRTPMYLHYLKTKPDHEERVNG----LHLLGRASEPIEQAQAAMWLLSDAASFVTG 247 Query: 242 QWVFVDGGYT 251 + VDGGYT Sbjct: 248 VTLPVDGGYT 257 Lambda K H 0.318 0.134 0.394 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: 133 Number of extensions: 5 Number of successful extensions: 3 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: 258 Length of database: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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: 47 (22.7 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