GapMind for Amino acid biosynthesis

 

Alignments for a candidate for Mt_cysM in Pseudomonas fluorescens FW300-N1B4

Align [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase (EC 2.5.1.113); O-phosphoserine sulfhydrylase (EC 2.5.1.65) (characterized)
to candidate Pf1N1B4_4889 Cystathionine beta-synthase (EC 4.2.1.22)

Query= BRENDA::P9WP53
         (323 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4889
          Length = 458

 Score =  173 bits (438), Expect = 8e-48
 Identities = 113/314 (35%), Positives = 164/314 (52%), Gaps = 28/314 (8%)

Query: 6   SLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEAD 65
           ++L+ +GNTPLV + R          GP   L+ KLE +NP GSIKDR  + MI+ AE D
Sbjct: 8   AVLELIGNTPLVRISRFDT-------GP-CTLFLKLESQNPGGSIKDRIGLAMIDTAERD 59

Query: 66  GLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAA 125
           G LRPG TI+E T+GNTG+ LA+  R KGYR++ V+P+  S E+   L+  GA++  + +
Sbjct: 60  GRLRPGGTIVEATAGNTGLGLALVGRAKGYRVVLVVPDKMSTEKVLHLKAMGAEVHITRS 119

Query: 126 E---GGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVA 181
           +   G  +     A  LA   P      Q+ NPAN  +H C T PE+ A    ++   V 
Sbjct: 120 DVGKGHPDYYQDVAARLARDIPDAFFADQFNNPANPLAHECSTAPEIWAQTQHDVDAIVV 179

Query: 182 GLGTTGTLMGTGRFLREHVANVKIVAAEP---------RYG----EGVYALRNMDEGFVP 228
           G+G+ GTL G  RF +    N+++V A+P         R G     G +A+  + E F+P
Sbjct: 180 GVGSAGTLTGLTRFFQRVQPNLEMVLADPVGSVMAEYSRSGTLGTPGSWAVEGIGEDFIP 239

Query: 229 ELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERAD 288
            + D   +   YS+   ++    R+L+  EGI  G STG +L AAL          E   
Sbjct: 240 SIADLSSVRKAYSISDEESFDHARQLLRAEGILGGSSTGTLLAAALRY---CREQTEPKR 296

Query: 289 IALVVADAGWKYLS 302
           +   V D G +YLS
Sbjct: 297 VVSFVCDTGTRYLS 310


Lambda     K      H
   0.317    0.134    0.398 

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: 370
Number of extensions: 17
Number of successful extensions: 5
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: 323
Length of database: 458
Length adjustment: 30
Effective length of query: 293
Effective length of database: 428
Effective search space:   125404
Effective search space used:   125404
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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