Align Short-chain dehydrogenase (characterized, see rationale)
to candidate CCNA_01892 CCNA_01892 short chain dehydrogenase
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__Caulo:CCNA_01892 Length = 546 Score = 115 bits (287), Expect = 3e-30 Identities = 91/256 (35%), Positives = 124/256 (48%), Gaps = 12/256 (4%) Query: 1 MDLNLQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALF 60 M Q +VV+VTGGA GIG A + A G +V R+ + R L P Sbjct: 26 MTSKAQSRVVLVTGGADGIGWAACQRFARAGDQVLVADRNVERAR--ERADSLGPDHHAI 83 Query: 61 QLELQDEARCGEAVAETVRRFGRLDGLVNNAGVND---SVGLDAGRNEFVASLERNLIHY 117 +++ EA+ E + R FGRLD LVNNAGV D + LD E N+ Sbjct: 84 AMDVSSEAQIREGFEQLHREFGRLDVLVNNAGVTDPQPTATLDQTAEEVARLQAINVTGA 143 Query: 118 YVMAHYCVP-HLKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGV 176 ++ A ++ GAI+N++S L + Y ASK A +SLTR A GV Sbjct: 144 FLAAREAGRLMIEQGHGAIINLASGAGLVALAKRTSYSASKAAVISLTRTLACEWAAKGV 203 Query: 177 RVNALIPAEVMTPLYEKWI-ATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGR 235 RVNA++P T + + I A +P + S+IPLG R EEMA+ A FL S Sbjct: 204 RVNAVLPGYTRTQMVQDQIDAGLLDP----SIVLSRIPLG-RMGEPEEMAEGAFFLASDA 258 Query: 236 SSHTTGQWVFVDGGYT 251 +S+ G + VDGGYT Sbjct: 259 ASYVVGATLVVDGGYT 274 Score = 86.7 bits (213), Expect = 1e-21 Identities = 71/246 (28%), Positives = 106/246 (43%), Gaps = 9/246 (3%) Query: 8 KVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQLELQDE 67 +V +TGG GIG + A G +V R + A G + Q ++ D Sbjct: 296 RVSAITGGGRGIGRCVVDLFHAAGDRLLVIERDAEGAKALAEALG--DEHIVVQADITDV 353 Query: 68 ARCGEAVAETVRRFGRLDGLVNNAGVND--SVGLDAGRNEFVASLERNLIHYYVMAHYCV 125 A A A+ R+GRLD L+NNAG D L+ +F + + N A Sbjct: 354 AAVEAAFAQAQARWGRLDVLINNAGAADVFKPSLEQTAQDFTSVYDLNFSGPLATAK-AA 412 Query: 126 PHLKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNALIPAE 185 L + G I+N+ S L + YCA+K A ++R A G+RVN + P Sbjct: 413 ARLMSQGGVIVNLGSIAGLGALPQRNAYCAAKAAVTMMSRSLACEWASAGIRVNTVAPGY 472 Query: 186 VMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTTGQWVF 245 + TP +A + + D I + P+G R E+A FL S +S+ G + Sbjct: 473 IETPAV---LALKSAGRAQFDKIRRRAPIG-RLGDPMEVARTIAFLASPAASYVAGATLT 528 Query: 246 VDGGYT 251 VDGG+T Sbjct: 529 VDGGWT 534 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: 318 Number of extensions: 15 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 258 Length of database: 546 Length adjustment: 30 Effective length of query: 228 Effective length of database: 516 Effective search space: 117648 Effective search space used: 117648 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: 50 (23.9 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