GapMind for Amino acid biosynthesis

 

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

Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Echvi_2080 Echvi_2080 Cystathionine beta-lyases/cystathionine gamma-synthases

Query= SwissProt::O31631
         (373 letters)



>lcl|FitnessBrowser__Cola:Echvi_2080 Echvi_2080 Cystathionine
           beta-lyases/cystathionine gamma-synthases
          Length = 381

 Score =  313 bits (801), Expect = 6e-90
 Identities = 166/374 (44%), Positives = 227/374 (60%), Gaps = 18/374 (4%)

Query: 7   TKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLEN 66
           TK+   G   D  TG +  PI+ ++ Y  +  G+  GF+Y RT NPTR  ++ +IA LEN
Sbjct: 5   TKVIHAGVAPDPTTGAIMTPIFQTSTYVQKSPGQHKGFEYSRTHNPTRDALQKSIAALEN 64

Query: 67  GARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFSDE 126
           G  GL FSSGM AI  ++ L   GDE+I ++DLYGGTYR+F   + KYG+ FH+    D 
Sbjct: 65  GKHGLCFSSGMGAIDALIKLLSPGDEVISTNDLYGGTYRIFTKVFAKYGIKFHFVSMDDP 124

Query: 127 DCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLEL 186
             +   I   T+ ++ ETPTNP+M   DI+ +A I  +H LLL VDNTF TP LQ PL+L
Sbjct: 125 ASIEKYINDKTRLIWAETPTNPMMNIIDIKALAAIAGKHDLLLGVDNTFATPYLQNPLDL 184

Query: 187 GADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMKT 246
           GAD+V+HS TKYL GH+D++ G +VV D+RL E++   QN+ GA   P D +L++RG+KT
Sbjct: 185 GADLVMHSVTKYLAGHSDVVMGALVVNDDRLAEDLAFIQNSCGATPGPQDCFLVLRGIKT 244

Query: 247 LSLRMRQHQANAQELAAFLEEQEEISDVLYPG----------------KGGMLSFRL--Q 288
           L LRM +H  N + +A +L    ++  V +PG                 GGM+SF +   
Sbjct: 245 LHLRMERHCQNGKTIAGYLRHHPKVDKVYWPGFEDHPNHDIAAKQMRDFGGMISFSIVGD 304

Query: 289 KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGI 348
           K+E     L+ L     AESLGGVES   +PA+ TH  IP+  R   G+ + L+R SVG+
Sbjct: 305 KQEDAKKVLENLHYFSLAESLGGVESLCGHPASMTHASIPKVEREKVGLTDSLIRLSVGV 364

Query: 349 EHAEDLKEDLKQAL 362
           E AEDLK DL  AL
Sbjct: 365 EDAEDLKNDLAAAL 378


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: 383
Number of extensions: 13
Number of successful extensions: 2
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: 381
Length adjustment: 30
Effective length of query: 343
Effective length of database: 351
Effective search space:   120393
Effective search space used:   120393
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: 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, 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