GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4430
          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 (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