GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Novosphingobium barchaimii LL02

Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_059153468.1 V474_RS22510 cystathionine beta-lyase

Query= SwissProt::O31631
         (373 letters)



>NCBI__GCF_001046635.1:WP_059153468.1
          Length = 411

 Score =  146 bits (368), Expect = 1e-39
 Identities = 122/403 (30%), Positives = 191/403 (47%), Gaps = 41/403 (10%)

Query: 1   MSQHVETKLAQIGNRSDEVTGTVSAPI-------YLSTAYRHRG--IGESTGFDYVRTKN 51
           + Q   T++   G RS+     V+ P+       Y  TA   +G    E   F Y R   
Sbjct: 15  LPQAPATRIVGAGRRSEWTGPVVNPPVWRASTHLYADTAALAQGPRTNEDGRFFYGRRGA 74

Query: 52  PTRQLVEDAIANLENGARG-LAFSSGMAAIQTIM-ALFKSGDELIVSSDLYGGTYRLFEN 109
           PT+  + DA+  +E GA G + + SG+AAI  +M  L + GD +++S + Y  T      
Sbjct: 75  PTQWALADALTAIEPGAAGTVLYPSGLAAIAGVMLTLLRPGDIVLISDNAYDPTRATGTG 134

Query: 110 EWKKYGLTFHYDDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLL 169
               +G+   + D  D           T+AV +E P +  M+  D+  +ARI +E G + 
Sbjct: 135 LLTDFGIEPRFFDPLDIAAYERLFCKRTRAVLLEAPGSLSMEMCDLPELARIAREKGAVS 194

Query: 170 IVDNTFYTPVLQRPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIG 229
           ++DNT+  P+    LE G DI + + TK++GGH+D++ G      E L  ++ Q    +G
Sbjct: 195 VLDNTWAGPLGFPALERGIDITLMALTKHVGGHSDVMMGSASAGPE-LYAKLRQRAQQLG 253

Query: 230 AVLPPFDSWLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYP------------ 277
            V+ P D+ L +RG++TL LR+R    +A  +A +L E+ E++ VL P            
Sbjct: 254 TVVSPDDAALTLRGLRTLHLRLRHEADSALAIARWLNERPEVAQVLCPMLPGAPGHDIWS 313

Query: 278 ----GKGGMLSFRLQKEEWV--NPFLKALKTICFAESLGGVESF---ITYPATQTHM--- 325
               G  G+ SF  +       N F+ AL       S GG ES    I   A ++ M   
Sbjct: 314 RDFSGGCGLFSFTFKGGTAAARNRFVDALTLFGIGYSWGGFESLVVPIDPSACRSRMAWP 373

Query: 326 DIPEEIRIANGVCNRLLRFSVGIEHAEDLKEDLKQALCQVKEG 368
             P E   ++GV     R ++G+E A DL  DL+QAL   +EG
Sbjct: 374 PHPHEAGDSHGV-----RLAIGLEDAGDLIADLEQALAAWREG 411


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: 329
Number of extensions: 25
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: 373
Length of database: 411
Length adjustment: 31
Effective length of query: 342
Effective length of database: 380
Effective search space:   129960
Effective search space used:   129960
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 26 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