GapMind for Amino acid biosynthesis

 

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

Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; Osteotoxin; EC 4.4.1.13 (characterized)
to candidate Pf1N1B4_4430 Cystathionine beta-lyase (EC 4.4.1.8)

Query= SwissProt::Q07703
         (396 letters)



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

 Score =  304 bits (779), Expect = 6e-87
 Identities = 168/394 (42%), Positives = 241/394 (61%), Gaps = 8/394 (2%)

Query: 4   TSAKHIDTLLQHLGSAPFNPDTGAAPVNLPSVRASTVRFQSLAKLEDAQRRKAAGERAST 63
           T    I T L H  SA     +G   VN+P  R STV F +LA++ DA+ R+ + ER  +
Sbjct: 530 TRDARIRTRLVH--SARTEKGSGGRAVNVPVTRLSTVLFDNLAQMRDARARRDS-ERVLS 586

Query: 64  YGRMGMDTHAALEQVFAELEGGTHCYLASSGLAGISMVFLSLLSAGEHALVADCAYGPVH 123
           YG  G  T  ALE +  ELEGG    L  +GLA ++  FL+ L  G+H L+ D  Y PV 
Sbjct: 587 YGARGNPTAFALEDLVTELEGGYRTRLYGTGLAAVAQTFLAYLRPGDHVLITDAVYAPVR 646

Query: 124 ELHEAVLSRLGIDVTFFDAKAD-LASLVRPTTRLIFAEAPGSLLFEMLDMPALARFAKQH 182
            L   +L   GI V++F      L + ++  T++++ E PGSLL+E+ D+PA+A   K  
Sbjct: 647 RLARELLEPFGIQVSYFAPDGSGLQAQLQANTKMVYTEVPGSLLYELCDLPAIAALCKPR 706

Query: 183 DLILATDNTWGSGYIYRPLTLGAQVSVIAGTKYVGGHSDLMLGAVVTNDEAIAKRLNRTQ 242
            ++LA DNTWGSGY+YRPLTLGA +S++A TKY+ GHSD+++G+V T  E + + L+   
Sbjct: 707 GILLAVDNTWGSGYLYRPLTLGADISIMALTKYLCGHSDVVMGSVCTRQE-VWQPLSSMS 765

Query: 243 YALGYSVSADDAWLALRGVRTMPVRMAQHARHALEVCEFLQNRPEVVRLYHPAWPADPGH 302
              G +VS DDA+L LRG RT+  R+  H R ALE+ ++LQ +P+V R++HPA P  P H
Sbjct: 766 DTFGIAVSPDDAYLVLRGARTLAPRLDVHERQALEIAQWLQAQPQVKRVFHPALPDHPHH 825

Query: 303 ALWQRDCSGSNGMLAVQLGLSPQA-ARDFVNALTLFGIGFSWGGFESLVQLVTPGELARH 361
           ALW+RD +GSNG+L+ +L  +       F++AL +FG+G SWGG+ESLV +    +  R+
Sbjct: 826 ALWRRDFNGSNGLLSFELREADATYVERFIDALQVFGLGASWGGYESLVTVADTKD--RN 883

Query: 362 QYWQGGSDALVRLHIGLESPADLIADLAQALDRA 395
                  + ++RLHIGLE    LI DL +    A
Sbjct: 884 SAADRALNPVLRLHIGLEDVDALIEDLQRGFAAA 917


Lambda     K      H
   0.321    0.134    0.403 

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: 879
Number of extensions: 38
Number of successful extensions: 6
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: 396
Length of database: 919
Length adjustment: 37
Effective length of query: 359
Effective length of database: 882
Effective search space:   316638
Effective search space used:   316638
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 (21.9 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