GapMind for Amino acid biosynthesis

 

Alignments for a candidate for moeZ in Shewanella loihica PV-4

Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate 5207513 Shew_0047 molybdopterin biosynthesis protein MoeB (RefSeq)

Query= SwissProt::P9WMN7
         (392 letters)



>FitnessBrowser__PV4:5207513
          Length = 255

 Score =  169 bits (429), Expect = 6e-47
 Identities = 95/244 (38%), Positives = 139/244 (56%), Gaps = 5/244 (2%)

Query: 15  LSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDF 74
           LS  E+ RYSRH+ I  +  +GQ+RLK A+VLVIGAGGLG  +  YLA AGVG + +VDF
Sbjct: 10  LSDAEILRYSRHISIKAMDFEGQERLKQAKVLVIGAGGLGCASTQYLAVAGVGQLTLVDF 69

Query: 75  DVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYD 134
           D V+ SNLQRQV+H  A +G+ K +SA+ S++ +NP +RV      L     + L  ++D
Sbjct: 70  DTVELSNLQRQVLHHDATIGQPKVESAKTSLMQLNPHLRVETINAVLDDEQILALVAEHD 129

Query: 135 LILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRDLYPEP 194
           L++D TDN   R  +N A      P V  +  R EG  +VF           Y  L+ + 
Sbjct: 130 LVMDCTDNIVVREQLNQACFQHKVPLVSAAAIRMEGTVTVFDYGEQSPCYHCYSKLFGD- 188

Query: 195 PPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTITI 254
                  +C E G+L  +   +  +   EAIK++  +G+TL GR+L+ DA+ M +R + +
Sbjct: 189 ----QQLTCVESGILAPVVGMIGCLQAVEAIKVLAKMGKTLSGRILMIDAMTMEFREMKL 244

Query: 255 RKDP 258
            K P
Sbjct: 245 PKQP 248


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: 211
Number of extensions: 8
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: 255
Length adjustment: 27
Effective length of query: 365
Effective length of database: 228
Effective search space:    83220
Effective search space used:    83220
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