GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Azoarcus sp. BH72

Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate WP_011765155.1 AZO_RS07195 O-acetylhomoserine aminocarboxypropyltransferase

Query= SwissProt::Q83A83
         (387 letters)



>NCBI__GCF_000061505.1:WP_011765155.1
          Length = 434

 Score =  228 bits (580), Expect = 3e-64
 Identities = 147/417 (35%), Positives = 218/417 (52%), Gaps = 42/417 (10%)

Query: 12  DTRVIHAGQKPDPLTGAVMTPIYTASTY----AQKSPGVHQ----GYEYSRSQNPTRFAY 63
           +T  +HAGQ PDP+ G+  TPI+  ++Y    A ++  +      G+ YSR  NPT    
Sbjct: 10  ETLALHAGQSPDPVHGSRATPIHFTTSYVFSDADQAAALFNLERPGHVYSRISNPTTAVL 69

Query: 64  ERCVADLESGQHGFAFASGMAAT-ATILELLQPGDHVVVMDDVYGGSYRLFENVRKRSAG 122
           E  VA LE G    A ASG AA    I  L+  G H+V    +YGGS+ L      R  G
Sbjct: 70  EERVAALEGGVGAIAVASGQAALHLAITTLMGAGGHIVASRALYGGSHNLLGYTLPRF-G 128

Query: 123 LSFSFVDFTDENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEKNIIAVADNTF 182
           +  +FVD  D +  R A+  +T++ + ES  NP L ++D+  ++ +A +  +  + D T 
Sbjct: 129 IHTTFVDPHDLDAWRAAIRPETRLFFGESVGNPGLDVLDIPAVSALAHQHRLPLLVDATL 188

Query: 183 ATPIIQRPLELGFDIVTHSATKYLNGHSDIIGGVAVVGDN---------KTLAEQ----- 228
            +P++QRPL+LG D+V HSATKYL GH   +GGV V G            TL E      
Sbjct: 189 VSPLLQRPLDLGADLVMHSATKYLGGHGVAVGGVIVDGGRFDWEASGLFPTLTEPYDGFH 248

Query: 229 ----------LKYLQNA-------IGAIAAPFDSFMVLRGLKTLAIRMERHCENAMQLAQ 271
                       +L  A        GA  +P ++F +L+GL+TL +RM  H  NA  +A+
Sbjct: 249 GMDFAEESPVAAFLLRARREGLRDFGACLSPMNAFQILQGLETLPLRMRAHVANARAVAE 308

Query: 272 WLEKHPKVKRVYYPGLPSHPQHSIAKKQMRY-FGGMISVELKCDLNETKKVLERCQLFTL 330
            L  HP V++V YPGLP H  H++A + + +  G ++S +LK      +  +   +LF+ 
Sbjct: 309 HLAAHPLVEKVAYPGLPGHRDHALAARLLPHGCGAVMSFDLKGGREGGRAFIGALRLFSH 368

Query: 331 AESLGGVESLIEHPAIMTHASIPQAERQKLGITDGFIRLSVGIEAITDLRHDLEAAL 387
             ++G  +SL+ HPA  TH  +  A+    GI +G +RLSVGIE   DL  DL+  L
Sbjct: 369 LANVGDAKSLVIHPASTTHFRMSAADLAAAGIGEGTVRLSVGIENTADLIADLDRGL 425


Lambda     K      H
   0.319    0.134    0.385 

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: 417
Number of extensions: 22
Number of successful extensions: 6
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: 387
Length of database: 434
Length adjustment: 31
Effective length of query: 356
Effective length of database: 403
Effective search space:   143468
Effective search space used:   143468
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: 50 (23.9 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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