Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate CCNA_01892 CCNA_01892 short chain dehydrogenase
Query= SwissProt::Q6CEE9 (278 letters) >FitnessBrowser__Caulo:CCNA_01892 Length = 546 Score = 129 bits (325), Expect = 1e-34 Identities = 81/248 (32%), Positives = 137/248 (55%), Gaps = 9/248 (3%) Query: 32 KGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTYGVRSKAYKCAV 91 + +V +TG + GIG+A + FA+AG V + + + E+A + + G A V Sbjct: 31 QSRVVLVTGGADGIGWAACQRFARAGDQVLV---ADRNVERARERADSLGPDHHAIAMDV 87 Query: 92 TNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVVDLDLNGAYYCA 151 ++ Q+ + + ++FG++D+ + NAG+ EE ++ +++ GA+ A Sbjct: 88 SSEAQIREGFEQLHREFGRLDVLVNNAGVTDPQPTATLDQTAEEVARLQAINVTGAFLAA 147 Query: 152 KYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSLAVEWAGFA-RC 210 + AG++ +QG+G+ I AS +G + + Y+A+K AV+ L+R+LA EWA R Sbjct: 148 REAGRLMIEQGHGAIINLASGAGLVALAKRTS--YSASKAAVISLTRTLACEWAAKGVRV 205 Query: 211 NTVSPGYMATE-ISDFIPRDTKEKWWQL--IPMGREGDPSELAGAYIYLASDASTYTTGA 267 N V PGY T+ + D I + L IP+GR G+P E+A +LASDA++Y GA Sbjct: 206 NAVLPGYTRTQMVQDQIDAGLLDPSIVLSRIPLGRMGEPEEMAEGAFFLASDAASYVVGA 265 Query: 268 DILVDGGY 275 ++VDGGY Sbjct: 266 TLVVDGGY 273 Score = 110 bits (274), Expect = 9e-29 Identities = 85/268 (31%), Positives = 133/268 (49%), Gaps = 23/268 (8%) Query: 12 TPLPTPVPKVSKNIMERFSLKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDE 71 TP P+P+ +V++ITG GIG V + F AG + + + E Sbjct: 285 TPAPSPLAP-----------SPRVSAITGGGRGIGRCVVDLFHAAGDRLLV---IERDAE 330 Query: 72 KAEYLSKTYGVRSKAYKCAVTNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVP 131 A+ L++ G + +T+ VE + +G++D+ I NAG P ++ Sbjct: 331 GAKALAEALGDEHIVVQADITDVAAVEAAFAQAQARWGRLDVLINNAGAADVFKPSLE-Q 389 Query: 132 NNEEWDKVVDLDLNGAYYCAKYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKC 191 +++ V DL+ +G AK A ++ + G + S++G + +PQ A Y AAK Sbjct: 390 TAQDFTSVYDLNFSGPLATAKAAARLMSQGGV--IVNLGSIAG-LGALPQRNA-YCAAKA 445 Query: 192 AVLHLSRSLAVEWAGFA-RCNTVSPGYMATEISDFIP---RDTKEKWWQLIPMGREGDPS 247 AV +SRSLA EWA R NTV+PGY+ T + R +K + P+GR GDP Sbjct: 446 AVTMMSRSLACEWASAGIRVNTVAPGYIETPAVLALKSAGRAQFDKIRRRAPIGRLGDPM 505 Query: 248 ELAGAYIYLASDASTYTTGADILVDGGY 275 E+A +LAS A++Y GA + VDGG+ Sbjct: 506 EVARTIAFLASPAASYVAGATLTVDGGW 533 Lambda K H 0.317 0.132 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: 363 Number of extensions: 18 Number of successful extensions: 8 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: 278 Length of database: 546 Length adjustment: 30 Effective length of query: 248 Effective length of database: 516 Effective search space: 127968 Effective search space used: 127968 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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