Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate SMc04043 SMc04043 hypothetical protein
Query= reanno::Smeli:SM_b21164 (271 letters) >FitnessBrowser__Smeli:SMc04043 Length = 293 Score = 103 bits (256), Expect = 6e-27 Identities = 74/246 (30%), Positives = 114/246 (46%), Gaps = 23/246 (9%) Query: 4 FEVRQGSS---PVILGFPHTGTDVPASIRERLN-DNGRILADTDWHIHDLYQGL-LPDAT 58 FEV + +S P + PH+G P ++ D I D + +L++ A Sbjct: 10 FEVLEPASQRIPFVFNSPHSGRHYPQFFLDQSRLDPHSIRRSEDHFVDELFRSATFLGAP 69 Query: 59 AVRATFHRYVIDANRDP---------------AGVSLYPGQNTTGLVPETDFDGLPIWKE 103 +RA F R +D NR+P A +S G VP + + I++ Sbjct: 70 LLRAHFPRAFLDVNREPYELDPRMFDGALPPHANISSMRVAGGLGTVPRLVAENMEIYR- 128 Query: 104 GEGPTEVDITERLRDFHAPYHAALSAEIARVKAIHGVVVLYDCHSIRSHIPFLFEGRLPD 163 G P E + ER+ + PYHA L IAR G+ +L DCHS+ ++ G PD Sbjct: 129 GRFPVEQAL-ERIETIYKPYHATLRKLIARTHVEFGMSILIDCHSMPGNVHLPGSGHRPD 187 Query: 164 FNIGTDMGKTCATEIERAAAEIAAGAECYSHILNGRFKGGWTTRHYGRPEQGVHAIQMEL 223 F IG G + A E+ R A E+ Y+ N + GG+ T HYGRP +G+HA+Q+E+ Sbjct: 188 FIIGDRYGTSAAAELSRVAVELLEQLG-YAVARNKPYAGGFITEHYGRPTRGLHALQIEI 246 Query: 224 AQSTHL 229 + ++ Sbjct: 247 NRGLYV 252 Score = 22.7 bits (47), Expect = 0.010 Identities = 12/34 (35%), Positives = 17/34 (50%) Query: 234 PPFALDRAKADRLRRPLKAILERIETVAKELKRT 267 P + + R R P++ LERIET+ K T Sbjct: 117 PRLVAENMEIYRGRFPVEQALERIETIYKPYHAT 150 Lambda K H 0.320 0.137 0.417 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: 214 Number of extensions: 13 Number of successful extensions: 4 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: 271 Length of database: 293 Length adjustment: 26 Effective length of query: 245 Effective length of database: 267 Effective search space: 65415 Effective search space used: 65415 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: 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