Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate WP_010962176.1 MCA_RS14635 KR domain-containing protein
Query= reanno::BFirm:BPHYT_RS16120 (260 letters) >NCBI__GCF_000008325.1:WP_010962176.1 Length = 251 Score = 101 bits (252), Expect = 1e-26 Identities = 76/253 (30%), Positives = 121/253 (47%), Gaps = 21/253 (8%) Query: 8 KVAILTGAASGIGEAVARRYLDEGARCVLV---DVKPADSFGDSLRATYGDRVLTVSADV 64 KVA++TGAA +G A+A D+G R ++ A + D L D + AD+ Sbjct: 11 KVALITGAARRVGAAIAAHLHDQGYRIIVHYHRSETDAATLCDDLNRRRDDSAAAIGADL 70 Query: 65 TRRDDIQRIVASTLERFGQIDILFNNAALFDMRPILEESWDVFDRLFAVNVKGMFFLMQ- 123 + ++ +VA+ R+G++D L NNA++F P+ + +D L N++ FFL+Q Sbjct: 71 LVLEALEPLVAAAARRWGRLDALVNNASVFYPTPMGSVTSQQWDELLGSNLRAPFFLVQH 130 Query: 124 AVAQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPHKINVNG 183 A+ +GC ++++ + + Y KA +++ T+S A LAP I VN Sbjct: 131 ALPWLSANRGCVVNLVDIHADRPLKNHPA---YSIAKAGLVALTRSLAKELAP-AIRVNA 186 Query: 184 IAPGVVDTPMWNEVDALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAALFLASADA 243 +APG + P + A NR +PLGR G P D+ A + A Sbjct: 187 VAPGAILWPEQGTDADVQAEILNR------------IPLGRPGTPLDVAKAVAWFLD-QA 233 Query: 244 DYITAQTLNVDGG 256 Y+T Q L VDGG Sbjct: 234 PYVTGQVLAVDGG 246 Lambda K H 0.321 0.135 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: 147 Number of extensions: 12 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: 260 Length of database: 251 Length adjustment: 24 Effective length of query: 236 Effective length of database: 227 Effective search space: 53572 Effective search space used: 53572 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 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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