GapMind for Amino acid biosynthesis

 

Alignments for a candidate for Mt_cysM in Pseudomonas simiae WCS417

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 GFF3937 PS417_20160 cysteine synthase

Query= BRENDA::P9WP53
         (323 letters)



>FitnessBrowser__WCS417:GFF3937
          Length = 300

 Score =  217 bits (552), Expect = 3e-61
 Identities = 120/305 (39%), Positives = 177/305 (58%), Gaps = 13/305 (4%)

Query: 3   RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQA 62
           +Y ++   +GNTPLV LQR++    +        L  KLE  NP GS+KDRPA+ MI +A
Sbjct: 4   QYPTIADCVGNTPLVRLQRMAGDTSN-------TLLLKLEGNNPAGSVKDRPALSMITRA 56

Query: 63  EADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIF 122
           E  G ++PG T++E TSGNTGI+LAMAA +KGY++I +MP+N S ER+  +  YGAQ+I 
Sbjct: 57  ELRGQIKPGDTLIEATSGNTGIALAMAAAIKGYKMILIMPDNGSAERKAAMTAYGAQLIL 116

Query: 123 SAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVA 181
              E G   A   A+ +AA     ++L Q+ N  N ++HY  TGPE+       ITHFV+
Sbjct: 117 VTQEDGMEGARDLAERMAAEGRG-LVLDQFANGDNPEAHYTSTGPEIWRQTQGTITHFVS 175

Query: 182 GLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYS 241
            +GTTGT+MG  R+L+E    ++IV  +P  G  +  +R   E ++P++Y+   +     
Sbjct: 176 SMGTTGTIMGNSRYLKEQNPAIQIVGLQPMEGSAIPGIRRWPEEYLPKIYNSSRVDRIID 235

Query: 242 VGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYL 301
           +   +A   TR L   EGIF G+S+G  +   L +        E A I  ++ D G +YL
Sbjct: 236 MAQREAEDTTRRLAREEGIFCGVSSGGAVAGMLRLSKEV----ENAVIVAIICDRGDRYL 291

Query: 302 STGAY 306
           STG +
Sbjct: 292 STGIF 296


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: 313
Number of extensions: 13
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: 300
Length adjustment: 27
Effective length of query: 296
Effective length of database: 273
Effective search space:    80808
Effective search space used:    80808
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: 48 (23.1 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