GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metY in Echinicola vietnamensis KMM 6221, DSM 17526

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate Echvi_2283 Echvi_2283 Cystathionine beta-lyases/cystathionine gamma-synthases

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



>lcl|FitnessBrowser__Cola:Echvi_2283 Echvi_2283 Cystathionine
           beta-lyases/cystathionine gamma-synthases
          Length = 391

 Score =  322 bits (824), Expect = 2e-92
 Identities = 163/381 (42%), Positives = 247/381 (64%), Gaps = 3/381 (0%)

Query: 19  TQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLEQ 78
           T+A+R  +++S   E S  +++TS + +D A +A   F+ +  G  YSR  NP    L +
Sbjct: 8   TEAVRIASSKSNQREHSAPIYMTSSFTFDSAEEARQMFAEEIPGNIYSRYANPNSSDLIE 67

Query: 79  RIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIET 138
           ++  +EG E   ATASGMAAM  ++   L  GDH++  R+ FGS   L     PK+GI +
Sbjct: 68  KVCAVEGTEDGIATASGMAAMFGSMASLLEQGDHILASRSLFGSTHQLLTRVFPKWGITS 127

Query: 139 TVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATP 198
           T  D  D + +   ++PNTK+ F ETP+NP ++V+DL+ +   A+   ++ VVDN FATP
Sbjct: 128 TYGDISDIENWDKLVKPNTKMLFIETPSNPGLEVIDLEWIGKFAKAHNLILVVDNCFATP 187

Query: 199 ALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAW 258
            LQ+P  +GAD+VA+SATK +DGQGRVL G + G +E I      F R+TGP++SPFNAW
Sbjct: 188 YLQQPAKWGADIVAHSATKYIDGQGRVLGGLILGKQELIKEVQF-FTRHTGPSISPFNAW 246

Query: 259 VVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSHPQHNLAMSQMAAAGPI 316
           ++ + +ETL +R++R   NAL VA + +    +  V +P L SHPQH+LA  QM   G I
Sbjct: 247 ILSRSMETLAIRMERHCANALAVASYFQDNKELEFVKYPFLKSHPQHDLAKKQMKHGGGI 306

Query: 317 FSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGM 376
            ++ L GG  +A   +D L +I ++ N+GD+RS++THPASTTHS + E++R  +G+  G+
Sbjct: 307 VTLTLKGGIERAQRFIDELQMITVTANLGDTRSIITHPASTTHSKLTEEERQRVGILPGL 366

Query: 377 LRLNVGLEDPEDLIADLDQAL 397
           +RL+ GLE  +D+IAD+++AL
Sbjct: 367 IRLSAGLEHHDDIIADIERAL 387


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: 383
Number of extensions: 12
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: 402
Length of database: 391
Length adjustment: 31
Effective length of query: 371
Effective length of database: 360
Effective search space:   133560
Effective search space used:   133560
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 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, the preprint on GapMind for carbon sources, 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