GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PSSH in Lacinutrix algicola AKS293

Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate WP_055437324.1 ASC41_RS14275 cysteine synthase family protein

Query= metacyc::MONOMER-20568
         (299 letters)



>NCBI__GCF_001418085.1:WP_055437324.1
          Length = 346

 Score =  216 bits (549), Expect = 8e-61
 Identities = 122/311 (39%), Positives = 178/311 (57%), Gaps = 20/311 (6%)

Query: 2   IYDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLH 61
           ++DN+L+ IGNTP++++  +    K    AK+E FNP  S KDRIAL +IEQAE +G L 
Sbjct: 7   VFDNVLDLIGNTPMIKLKKMTSEFKGNFLAKVEAFNPGHSSKDRIALYIIEQAEKQGILK 66

Query: 62  PGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGT 121
           PG TIIE TSGNTG  +AM+  +KGY+ I+ +S   S ++  M+K  GA++ +    +  
Sbjct: 67  PGDTIIETTSGNTGFSIAMVSVIKGYDCILAVSSKSSADKIDMLKNMGAKVYVCPANVSA 126

Query: 122 DG--AIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGT 179
           D   +  +VA+ + +        NQ+ N+ N  AHY +T  EIW QT G +TH VA  GT
Sbjct: 127 DDPRSYYQVAKRLHDEMKGSVYINQYFNQLNIDAHYASTGPEIWNQTNGKITHLVACSGT 186

Query: 180 SGTLMGVGKNLREKNPEIKIIEAQ---------------PTKGHYIQGLKSMEEAIVPAI 224
            GT+ G  K L+E+NP IKII                    K  Y   ++ + + ++P  
Sbjct: 187 GGTISGTAKYLKEQNPNIKIIGVDAFGSVLKKYHETREFDDKEIYPYRIEGLGKNLIPTA 246

Query: 225 YQADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLA---EKIDSGVIVV 281
              D IDE + +  EE+   AREI   EG+F+G +SGAAM A ++L+   E  +S  IVV
Sbjct: 247 TDFDTIDEFVKVTDEESAHTAREIAKTEGLFVGYTSGAAMQAIKQLSASGEFKESDNIVV 306

Query: 282 LFADRGEKYLS 292
           +F D G +Y+S
Sbjct: 307 IFPDHGSRYMS 317


Lambda     K      H
   0.315    0.133    0.367 

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: 331
Number of extensions: 21
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: 299
Length of database: 346
Length adjustment: 28
Effective length of query: 271
Effective length of database: 318
Effective search space:    86178
Effective search space used:    86178
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: 42 (22.0 bits)
S2: 48 (23.1 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