GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Geobacter metallireducens GS-15

Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_004514089.1 GMET_RS03505 PLP-dependent aspartate aminotransferase family protein

Query= SwissProt::O31631
         (373 letters)



>NCBI__GCF_000012925.1:WP_004514089.1
          Length = 391

 Score =  361 bits (926), Expect = e-104
 Identities = 189/377 (50%), Positives = 250/377 (66%), Gaps = 19/377 (5%)

Query: 4   HVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIAN 63
           ++ T+ AQIG   D  TG V+ PIY +  +RH G+G+STG+DY R+ NPTRQ +E+ IA 
Sbjct: 2   NIATQTAQIGLEWDTRTGAVTVPIYQTATFRHPGLGQSTGYDYTRSGNPTRQALEEGIAR 61

Query: 64  LENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDF 123
           LE GARG A++SGMAAI  ++ LFK GD L+V+ DLYGGT RLF+  + +Y L+F Y D 
Sbjct: 62  LEGGARGFAYASGMAAIANLLLLFKKGDHLVVTEDLYGGTCRLFDQIFTQYELSFTYVDT 121

Query: 124 SDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRP 183
           SD   +R+ I P TKA+FVE+ TNPL++ ADI  ++ + +E GLL IVDNTF TP L RP
Sbjct: 122 SDIKAVRAAIRPETKALFVESLTNPLLKVADIAALSALCRERGLLHIVDNTFLTPYLLRP 181

Query: 184 LELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRG 243
            + GADI ++SATKYL GHND ++GLV VKD +L E ++  QN++GAVL P DSWL +RG
Sbjct: 182 FDHGADITVYSATKYLAGHNDTVSGLVAVKDPQLAERVYFLQNSVGAVLGPQDSWLTIRG 241

Query: 244 MKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK-------------------GGMLS 284
           MKTLS+R+ + Q NA  +A +L     +  V YPG                    G M++
Sbjct: 242 MKTLSVRLDRQQENAGRVAQWLSNHPRVRKVYYPGLSGHPGHPGHELLARQARGFGAMIA 301

Query: 285 FRLQKEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRF 344
           F + +   V   L   + I FAESLGGVE+ IT+P  QTH DIP E+R   G+ + LLR 
Sbjct: 302 FEVDEHALVERLLLKTEVISFAESLGGVETLITFPQVQTHADIPPELRQRLGINDVLLRL 361

Query: 345 SVGIEHAEDLKEDLKQA 361
           SVGIE A+DL +DL QA
Sbjct: 362 SVGIEDADDLIDDLAQA 378


Lambda     K      H
   0.319    0.135    0.392 

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: 431
Number of extensions: 14
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: 373
Length of database: 391
Length adjustment: 30
Effective length of query: 343
Effective length of database: 361
Effective search space:   123823
Effective search space used:   123823
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: 50 (23.9 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