GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Shewanella sp. ANA-3

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate 7025253 Shewana3_2414 cystathionine beta-lyase (RefSeq)

Query= reanno::Korea:Ga0059261_3194
         (402 letters)



>FitnessBrowser__ANA3:7025253
          Length = 399

 Score =  170 bits (430), Expect = 8e-47
 Identities = 128/391 (32%), Positives = 189/391 (48%), Gaps = 16/391 (4%)

Query: 11  ITQNWKPATQAIRGGTARSEW--GETSEALFLTSGYAYDCAGDAAARFSGDQQG-MTYSR 67
           +T   + ATQ +  G  + +W  G  +  +F  S   +D   D          G M Y R
Sbjct: 1   MTDKHQLATQIVSVGRDK-KWTKGVINPPVFRASTIVFDTMEDMRHAAKNKTNGEMFYGR 59

Query: 68  LQNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLT 127
              PT    +  I+ LEG        SG AA++AALL  L AGDHL+   + +   R L 
Sbjct: 60  RGTPTHFAFQAAISELEGGAGTALYPSGAAAISAALLSFLQAGDHLLMVDSVYEPTRDLC 119

Query: 128 DTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGI 187
              L  F IETT  D    +   + IRPNTKV F E+P + TM+V D+  +C IA E G+
Sbjct: 120 SHILAGFNIETTYYDPLIGEGIRELIRPNTKVLFLESPGSITMEVQDVPTLCRIAHEHGL 179

Query: 188 VTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRN 247
           VT++DN +A+P   +P + G DV   +ATK + G   V+ G     E+     L      
Sbjct: 180 VTILDNTWASPINSKPFEMGVDVSIQAATKYIVGHSDVMIGTATANEKHWPQ-LRERSYL 238

Query: 248 TGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNL 305
            G T SP + ++  +GL TL +R+ +  +NALKVA +L+ R  V  +  P   + P H  
Sbjct: 239 LGQTTSPDDVYLATRGLRTLGVRMAQHEKNALKVANWLKTRPEVDHLRHPAFDTCPGHEF 298

Query: 306 AMSQMAAAGPIFSIELDGGRTQA-HGLLDALGLIDISNNIGDSRSLM--THPASTTHSGV 362
                +AA  +FS  L  G  +A   L++ +    +  + G   SL+          S  
Sbjct: 299 FKRDFSAANGLFSFVLKQGDQEAVTALVENMQHFKMGFSWGGYESLILGIFGIEKIRSAT 358

Query: 363 AEDQRLLMGVGEGMLRLNVGLEDPEDLIADL 393
             D R      + ++R+++GLEDP+DLIADL
Sbjct: 359 QWDAR------KPLIRVHIGLEDPDDLIADL 383


Lambda     K      H
   0.319    0.134    0.396 

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: 333
Number of extensions: 18
Number of successful extensions: 4
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: 402
Length of database: 399
Length adjustment: 31
Effective length of query: 371
Effective length of database: 368
Effective search space:   136528
Effective search space used:   136528
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: 50 (23.9 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