GapMind for Amino acid biosynthesis

 

Alignments for a candidate for mesB in Carboxydothermus pertinax Ug1

Align [corrinoid iron-sulfur protein]-dependent methionine synthase (characterized)
to candidate WP_075858214.1 cpu_RS01415 methionine synthase

Query= metacyc::MONOMER-21502
         (342 letters)



>NCBI__GCF_001950255.1:WP_075858214.1
          Length = 346

 Score =  173 bits (438), Expect = 7e-48
 Identities = 113/337 (33%), Positives = 173/337 (51%), Gaps = 18/337 (5%)

Query: 9   LPTMIGSMPHTDPKAAVDIITHYLQDIPVWPQLPRRSCLEGMSAQFSQGLPGVKINQ--- 65
           L T IGSMP  D K  ++II   L  IP WPQ+P+R   E    QF + L  V + Q   
Sbjct: 5   LKTGIGSMPLVDVKKNLEIIKKALPQIPHWPQMPQRGIAEHFVFQFLRPLTEVGLLQVEG 64

Query: 66  DKVWIEPNPSFESELESLYQAYLD----NDFNKFPIGAEYAAGLYELASRN----LSPLL 117
           +K   + + +F  +L   Y+ Y +     D+  F +  E   GLY L  +      + L 
Sbjct: 65  NKGIFKKDETFPEKLTFFYEKYFEALEKRDYAFFAMPRESGEGLYYLVEKFNESFSAALA 124

Query: 118 VKGHITGPLTYCMSIKDPSGKDILYDEVLSDAATKLLKLKATWQEHFLRNICRNTIIFVD 177
           VKG + GPL+  +++ D +     YD  + +A  K L + A WQ +FL+   R   +FVD
Sbjct: 125 VKGQMAGPLSILLTLTDENKIPAFYDPEIREAVVKTLVMSARWQVNFLKTTGRMVYLFVD 184

Query: 178 EPAMSAYGS-AYLPLSREQVTGMFDEVFSGI---SGLKGVHCCGNTDWSILMDTRVDIIN 233
           +PA++ YGS  +L L RE+V G+  E+ + I    G+ GVH C   DWSI+ +    +I+
Sbjct: 185 DPAIANYGSFTHLTLKREEVVGVLKEIIAAILEEGGVPGVHSCAGIDWSIVTEAGAKVIS 244

Query: 234 FDTYAYANSLSIYTDEVKAFIKRGGAVAWGIVPTDEKALKEETAASLKDRLEAAMSHFDS 293
            D   Y +SL  Y +EVK+ +  GG +A GI+PT  + ++  +   L    E  ++    
Sbjct: 245 VDAANYLDSLFPYKEEVKSLLSAGGILALGIIPTGPE-IENYSLEDLYADFEKKVNLLRE 303

Query: 294 HGLPFAELARHSLITPACGLGLKSPEAAERAPQLLAE 330
            G+   +     ++TPACG GL  PE AE+   LL +
Sbjct: 304 MGVVTND--SMLMLTPACGTGLLPPEQAEKIYSLLRD 338


Lambda     K      H
   0.319    0.135    0.409 

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: 290
Number of extensions: 17
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: 342
Length of database: 346
Length adjustment: 29
Effective length of query: 313
Effective length of database: 317
Effective search space:    99221
Effective search space used:    99221
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: 49 (23.5 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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