GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Clostridium kluyveri DSM 555

Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_012102527.1 CKL_RS10715 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase

Query= BRENDA::Q187D4
         (421 letters)



>NCBI__GCF_000016505.1:WP_012102527.1
          Length = 428

 Score =  439 bits (1128), Expect = e-127
 Identities = 208/422 (49%), Positives = 296/422 (70%), Gaps = 3/422 (0%)

Query: 2   YNKETICVQGNYKPGNGEPRVLPLYQSTTFKYSSIDQLAELFDLKVDGHIYSRISNPTIQ 61
           Y   T CVQ  Y+PGNGEPR +P+ QSTTFKY++ + + +LFDL+  G+ YSR+ NPT  
Sbjct: 4   YKINTKCVQAGYRPGNGEPRQVPIIQSTTFKYNTSEDMGKLFDLEASGYFYSRLQNPTND 63

Query: 62  AFEEKISLLEGGVSSVAVSSGQSANMLAVLNICKSGDSILCSSKVYGGTFNLLGPSLKKF 121
              +KI+ +E G +++  SSGQ+AN  A+ NIC  GD I+ SS +YGGTFNL+  ++ K 
Sbjct: 64  YVAQKIADMESGTAAMLTSSGQAANFFALFNICNCGDHIVASSSIYGGTFNLISVTMSKM 123

Query: 122 GIDLISFDLDSSEDEIVELAKENTKVVFAETLANPTLEVIDFEKIANVAKRINVPFIVDN 181
           GI       D +E+E+    + NTK VF ET+ANP L V+D EK A  A   +VP IVDN
Sbjct: 124 GITTTFVSPDCTEEELNAAFQTNTKAVFGETIANPALTVLDIEKFAKAAHAHDVPLIVDN 183

Query: 182 SLASPVLCNPLKYGANIVTHSTTKYLDGHASSVGGIIVDGGNFNW--DNGKFPELVEPDP 239
           +  +P+ C P ++GA+IVTHSTTKY+DGH ++VGG+IVD GNF+W     KFP L  PD 
Sbjct: 184 TFPTPINCRPFEWGADIVTHSTTKYMDGHGAAVGGVIVDSGNFDWMAHADKFPGLCTPDD 243

Query: 240 TYHGISYTQKFG-NAAYATKARVQLLRDYGNCLSPFNAYLTNLNVETLHLRMERHSENAL 298
           +YHGI+Y +KFG   A+ TK   QL+RD+G+  SP +A++ NL +E+LH+RM RH EN  
Sbjct: 244 SYHGITYAEKFGKEGAFITKCTAQLMRDFGSIQSPQHAFILNLGLESLHVRMPRHCENGQ 303

Query: 299 KIARFLEKHENVDWINYPGLEDNKYYENAKKYLSRGCSGVLSFGVRGGLENAKKFVEKLQ 358
            +A FL+ H  V ++NY GL  +KYY+ A+KYL  G  GV+SFG++GG E A+ F++ L+
Sbjct: 304 AVAEFLQNHPKVAYVNYCGLPGDKYYKIAQKYLPNGSCGVVSFGLKGGREEAEIFMKNLK 363

Query: 359 IASLVTHVSDVRTCVIHPASTTHRQLTEEQLIASGVLPSLIRLSVGIENVEDLIADLNQA 418
           + ++ THV+D R+C ++PA++THRQ+ +E+L  +GV   LIR+S GIE+ EDLI D++Q+
Sbjct: 364 LVAIETHVADARSCCLNPATSTHRQMNDEELKEAGVPAELIRISCGIEDKEDLIYDISQS 423

Query: 419 LN 420
           L+
Sbjct: 424 LD 425


Lambda     K      H
   0.316    0.135    0.387 

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: 515
Number of extensions: 14
Number of successful extensions: 3
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: 421
Length of database: 428
Length adjustment: 32
Effective length of query: 389
Effective length of database: 396
Effective search space:   154044
Effective search space used:   154044
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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