GapMind for Amino acid biosynthesis

 

Alignments for a candidate for moeZ in Escherichia coli BW25113

Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate 18024 b3992 thiamin biosynthesis, thiazole moiety (VIMSS)

Query= SwissProt::P9WMN7
         (392 letters)



>FitnessBrowser__Keio:18024
          Length = 251

 Score =  155 bits (393), Expect = 9e-43
 Identities = 89/247 (36%), Positives = 138/247 (55%), Gaps = 6/247 (2%)

Query: 15  LSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDF 74
           ++  +  RYSR +++ D+ +DGQ++L +++VL+IG GGLG P  LYLA AGVGT+ + D 
Sbjct: 1   MNDRDFMRYSRQILLDDIALDGQQKLLDSQVLIIGLGGLGTPAALYLAGAGVGTLVLADD 60

Query: 75  DVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYD 134
           D V  SNLQRQ++    D+ R K+Q ++  +  +NP I++   + RL      D   + D
Sbjct: 61  DDVHLSNLQRQILFTTEDIDRPKSQVSQQRLTQLNPDIQLTALQQRLTGEALKDAVARAD 120

Query: 135 LILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRDLYPEP 194
           ++LD TDN ATR  +N A V    P +  S   F GQ  V       G    YR L+P+ 
Sbjct: 121 VVLDCTDNMATRQEINAACVALNTPLITASAVGFGGQLMVLTPPWEQGC---YRCLWPDN 177

Query: 195 PPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTITI 254
             P    +C   GV+G +   + ++   EAIKL++GI ET  G L ++D     +R++ +
Sbjct: 178 QEPER--NCRTAGVVGPVVGVMGTLQALEAIKLLSGI-ETPAGELRLFDGKSSQWRSLAL 234

Query: 255 RKDPSTP 261
           R+    P
Sbjct: 235 RRASGCP 241


Lambda     K      H
   0.319    0.137    0.404 

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: 260
Number of extensions: 16
Number of successful extensions: 2
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: 392
Length of database: 251
Length adjustment: 27
Effective length of query: 365
Effective length of database: 224
Effective search space:    81760
Effective search space used:    81760
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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