GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metZ in Pseudomonas fluorescens FW300-N1B4

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Pf1N1B4_4430 Cystathionine beta-lyase (EC 4.4.1.8)

Query= SwissProt::P55218
         (403 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4430 Cystathionine
           beta-lyase (EC 4.4.1.8)
          Length = 919

 Score =  189 bits (479), Expect = 4e-52
 Identities = 129/382 (33%), Positives = 202/382 (52%), Gaps = 18/382 (4%)

Query: 30  RTPEGEHGEALFTT----SSYVFRTAA---DAAARFAGEVPGNVYSRYTNPTVRTFEERI 82
           RT +G  G A+       S+ +F   A   DA AR   E   + Y    NPT    E+ +
Sbjct: 544 RTEKGSGGRAVNVPVTRLSTVLFDNLAQMRDARARRDSERVLS-YGARGNPTAFALEDLV 602

Query: 83  AALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQVDY 142
             LEG  +     +G++A+    ++    GDHVL++ +V+     L  +  + FGIQV Y
Sbjct: 603 TELEGGYRTRLYGTGLAAVAQTFLAYLRPGDHVLITDAVYAPVRRLARELLEPFGIQVSY 662

Query: 143 PPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTPAL 202
               D +  +A  + NTK+ + E P + L EL D+ A+A +   +G LLAVDN + +  L
Sbjct: 663 FA-PDGSGLQAQLQANTKMVYTEVPGSLLYELCDLPAIAALCKPRGILLAVDNTWGSGYL 721

Query: 203 QQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTAGPTLSPFNAWLFL 262
            +PL LGAD+ I + TKY+ G    + G V  R E  + +     T G  +SP +A+L L
Sbjct: 722 YRPLTLGADISIMALTKYLCGHSDVVMGSVCTRQEVWQPLSSMSDTFGIAVSPDDAYLVL 781

Query: 263 KGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGAVVSF 322
           +G  TL  R+  H   AL +A+WL+ QP ++RV++  LP HP H L RR  +G   ++SF
Sbjct: 782 RGARTLAPRLDVHERQALEIAQWLQAQPQVKRVFHPALPDHPHHALWRRDFNGSNGLLSF 841

Query: 323 DVKGGRDAAW--RFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSLI 380
           +++   DA +  RFIDA ++  +  + G  ++ +      +  R S  DRA     + ++
Sbjct: 842 ELREA-DATYVERFIDALQVFGLGASWGGYESLVT--VADTKDRNSAADRAL----NPVL 894

Query: 381 RVAVGLEDLDDLKADMARGLAA 402
           R+ +GLED+D L  D+ RG AA
Sbjct: 895 RLHIGLEDVDALIEDLQRGFAA 916


Lambda     K      H
   0.319    0.133    0.392 

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: 793
Number of extensions: 40
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: 403
Length of database: 919
Length adjustment: 37
Effective length of query: 366
Effective length of database: 882
Effective search space:   322812
Effective search space used:   322812
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: 53 (25.0 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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