Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate 350543 BT1015 putative oxidoreductase (NCBI ptt file)
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__Btheta:350543 Length = 295 Score = 97.4 bits (241), Expect = 3e-25 Identities = 75/246 (30%), Positives = 114/246 (46%), Gaps = 19/246 (7%) Query: 15 ITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQTA 74 +TGGA G+G A E G D+ G+ A+ G +F P DV+ ++ +++ Sbjct: 58 VTGGAEGIGRAIVEAFCKDGHQVAFCDINAVSGQQTARDTG--AIFHPVDVSDKEALESC 115 Query: 75 LALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLVAG 134 + ++ +D+ +N GI+ S ++EDF ++L VNL F RL+A Sbjct: 116 MQQILDEWKDIDIVINNVGISKFSSITET------SVEDFDKILSVNLRPVFITSRLLA- 168 Query: 135 EMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVM 194 + + G IIN S + G Y+ASKGGI +T +A L+ I V Sbjct: 169 -IHRKAQSDSNPYGRIINICSTRYLMSEPGSEGYAASKGGIYSLTHALALSLSEWNITVN 227 Query: 195 TIAPGLFGTPLLTSL-PEKVCNFLASQVPFPSRLGDPAEYAHLVQAII--ENPFLNGEVI 251 +IAPG T L PE SQ P R+G P + A + + EN F+NGE I Sbjct: 228 SIAPGWIQTQNYDQLRPED-----HSQHP-SRRVGKPEDIARMCLFLCRDENDFINGENI 281 Query: 252 RLDGAI 257 +DG + Sbjct: 282 TIDGGM 287 Lambda K H 0.318 0.135 0.385 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: 155 Number of extensions: 6 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: 261 Length of database: 295 Length adjustment: 25 Effective length of query: 236 Effective length of database: 270 Effective search space: 63720 Effective search space used: 63720 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: 47 (22.7 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