Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate Ac3H11_2939 D-arabinitol 4-dehydrogenase (EC 1.1.1.11)
Query= curated2:P39160 (486 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2939 Length = 463 Score = 220 bits (561), Expect = 7e-62 Identities = 140/394 (35%), Positives = 207/394 (52%), Gaps = 12/394 (3%) Query: 25 IVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMP--GNDRVLIENLKKQQLLYTVA 82 I+HLG G+FHRAHQA+Y H L + +DW I NL P + ++ + L TV Sbjct: 4 ILHLGLGSFHRAHQAVYMHQLRQQGSTDWAIAGGNLRPDMADTIAALQAQGGRYTLETVT 63 Query: 83 EKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGYCADAASGQLD 142 +G S +I S++ + P D ++ A A P T I+S TVTE GY DAA+ QLD Sbjct: 64 PQGERS--YTVIESIQRVI-PYQDDLAPLIAAGADPATRIISFTVTEAGYYLDAAN-QLD 119 Query: 143 LNNPL-IKHDLENPTAPKSA---IGYIVEALRLRREKGLKAFTVMSCDNVRENGHVAKVA 198 ++ DL A ++ G + LR R G T+M+CDN+R NG ++ Sbjct: 120 WATFADLRADLATVQAGQAGHTIYGGLASILRARMRAGAGPVTLMNCDNLRHNGDRSRGG 179 Query: 199 VLGLAQAR-DPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIACEPF 257 +L A D L W+E+N T P MVDRI P TP+ + + G D A+ E F Sbjct: 180 LLQFIDALGDAPLKGWVEQNTTSPNAMVDRITPRPTPDVAERVKTATGWDDKAALMGESF 239 Query: 258 RQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYETIADT 317 QWVIED+F+ GRP W+KVG + V V E K+R+LN +HS +A+ G L GY+ I + Sbjct: 240 IQWVIEDDFIAGRPAWEKVGVEMVQSVQAHEEAKIRLLNATHSCIAWAGTLAGYQYIHEG 299 Query: 318 VTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMDGSQK 377 + A R+ A + + P L +P DL AY ++++RF NP++ ++AMD K Sbjct: 300 THDAAIRQMAHDYVTDDAIPVL-LPCPIDLEAYRDVVLDRFGNPAIADTNQRVAMDAFSK 358 Query: 378 LPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQ 411 +P + +R L + +A+ A ++ Y Q Sbjct: 359 IPGMIAPTIRDKLARNQPFDSVAVLPALFLAYLQ 392 Lambda K H 0.320 0.135 0.408 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: 604 Number of extensions: 27 Number of successful extensions: 5 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: 486 Length of database: 463 Length adjustment: 33 Effective length of query: 453 Effective length of database: 430 Effective search space: 194790 Effective search space used: 194790 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 (21.8 bits) S2: 51 (24.3 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