GapMind for Amino acid biosynthesis

 

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

Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Pf1N1B4_4430 Cystathionine beta-lyase (EC 4.4.1.8)

Query= SwissProt::O31631
         (373 letters)



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

 Score =  167 bits (424), Expect = 8e-46
 Identities = 106/329 (32%), Positives = 174/329 (52%), Gaps = 27/329 (8%)

Query: 51  NPTRQLVEDAIANLENGARGLAFSSGMAAI-QTIMALFKSGDELIVSSDLYGGTYRLFEN 109
           NPT   +ED +  LE G R   + +G+AA+ QT +A  + GD ++++  +Y    RL   
Sbjct: 592 NPTAFALEDLVTELEGGYRTRLYGTGLAAVAQTFLAYLRPGDHVLITDAVYAPVRRLARE 651

Query: 110 EWKKYGLTFHYDDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLL 169
             + +G+   Y    D   L++++  NTK V+ E P + L +  D+  IA + K  G+LL
Sbjct: 652 LLEPFGIQVSYFA-PDGSGLQAQLQANTKMVYTEVPGSLLYELCDLPAIAALCKPRGILL 710

Query: 170 IVDNTFYTPVLQRPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIG 229
            VDNT+ +  L RPL LGADI I + TKYL GH+D++ G V  + E + + +    +  G
Sbjct: 711 AVDNTWGSGYLYRPLTLGADISIMALTKYLCGHSDVVMGSVCTRQE-VWQPLSSMSDTFG 769

Query: 230 AVLPPFDSWLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYP------------ 277
             + P D++L++RG +TL+ R+  H+  A E+A +L+ Q ++  V +P            
Sbjct: 770 IAVSPDDAYLVLRGARTLAPRLDVHERQALEIAQWLQAQPQVKRVFHPALPDHPHHALWR 829

Query: 278 ----GKGGMLSFRLQKEE--WVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEI 331
               G  G+LSF L++ +  +V  F+ AL+      S GG ES +T        D  +  
Sbjct: 830 RDFNGSNGLLSFELREADATYVERFIDALQVFGLGASWGGYESLVTV------ADTKDRN 883

Query: 332 RIANGVCNRLLRFSVGIEHAEDLKEDLKQ 360
             A+   N +LR  +G+E  + L EDL++
Sbjct: 884 SAADRALNPVLRLHIGLEDVDALIEDLQR 912


Lambda     K      H
   0.319    0.135    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: 761
Number of extensions: 41
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: 373
Length of database: 919
Length adjustment: 36
Effective length of query: 337
Effective length of database: 883
Effective search space:   297571
Effective search space used:   297571
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 (21.7 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