Align NADH-dependent aldehyde reductase (EC 1.1.1.77; EC 1.1.1.244; EC 1.1.1.1) (characterized)
to candidate H281DRAFT_02547 H281DRAFT_02547 Nucleoside-diphosphate-sugar epimerase
Query= metacyc::G3O-32155-MONOMER (298 letters) >FitnessBrowser__Burk376:H281DRAFT_02547 Length = 297 Score = 238 bits (606), Expect = 2e-67 Identities = 127/296 (42%), Positives = 177/296 (59%), Gaps = 4/296 (1%) Query: 1 MKVFITGASGFIGSAVLSELISSGHEVVGLARSDEAAAKIKSIDPAAKILRGDLKDLEIL 60 M++ +TGASG+IGSA ++ELI +GH V+GLAR+DEAAAKI ++ A+++RG L +L+ L Sbjct: 1 MRILVTGASGWIGSASVTELIDAGHHVLGLARNDEAAAKIAAL--GAEVVRGSLDNLDSL 58 Query: 61 KKGATESDGVIHLGFVHDFKNFEQCCEIDRQATVAMLESLKGSNKPFLYTNGTLSLRPNK 120 + AT ++GV+HLG+ HDF + DR A + L G+ P L +GTL L + Sbjct: 59 RVAATMAEGVVHLGYNHDFSQMAAAAQTDRAAIETFADVLTGTGGPLLIASGTLGLATGR 118 Query: 121 VANEQDGIDEDSKILRAVTEQVALSYKDKGVSARIVRLPFSVHGKG-DKAFVPILMNIAK 179 V E D D R L +++G+ + +VR +VHG G D FV +L IA+ Sbjct: 119 VGIESDTPAPDGHP-RLANAAYVLGLRERGIRSMVVRFAPTVHGAGGDHGFVAVLARIAR 177 Query: 180 AAGKSGYVGQGTNAWAAVHRLDTAPLFRLVLEKGKTGQVYHCVGEQGIPFKDIARVIGEI 239 +G S Y+G G N W AV+RLD L RL ++K G H V E+G+ ++IA +G Sbjct: 178 QSGASAYIGDGQNRWPAVNRLDAGKLVRLAVDKAPAGSALHAVAEEGVATREIAGALGRF 237 Query: 240 LNVPVASIPVDDAESHFGFLTCFVTRDGPVSSEGTRKELGWQPQQIGLLEDIRANY 295 LNVPV SIP D A+S F +L+ F D P SS TR LGW+P LLEDI A + Sbjct: 238 LNVPVESIPADQAQSRFDWLSMFFGADIPASSAHTRSLLGWEPVHPTLLEDIAAGH 293 Lambda K H 0.318 0.136 0.393 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: 256 Number of extensions: 10 Number of successful extensions: 4 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: 298 Length of database: 297 Length adjustment: 26 Effective length of query: 272 Effective length of database: 271 Effective search space: 73712 Effective search space used: 73712 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: 48 (23.1 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