GapMind for Amino acid biosynthesis

 

Aligments for a candidate for CGL in Dyella japonica UNC79MFTsu3.2

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate N515DRAFT_4305 N515DRAFT_4305 cystathionine gamma-lyase

Query= BRENDA::Q5H4T8
         (397 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_4305 N515DRAFT_4305
           cystathionine gamma-lyase
          Length = 392

 Score =  571 bits (1471), Expect = e-167
 Identities = 274/383 (71%), Positives = 322/383 (84%), Gaps = 1/383 (0%)

Query: 11  GDRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYE 70
           G  +L L TLAIH GQSPDP+TGA+M PIYATSTY Q SPG+H+G+EYSRT NPTR AYE
Sbjct: 10  GQSSLGLGTLAIHAGQSPDPTTGAIMTPIYATSTYVQESPGKHKGYEYSRTQNPTRMAYE 69

Query: 71  RCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLD 130
            CVAALEGG   FAF SG+AA +TV++LLD+GSHV+AMDDLYGG++RLFERVRRR+AGLD
Sbjct: 70  ACVAALEGGVAGFAFGSGLAAAATVLDLLDSGSHVIAMDDLYGGSYRLFERVRRRSAGLD 129

Query: 131 FSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFAS 190
           F+FVDL D  A KAA++ +TKM+W ETPTNPMLKLVD+A +A  A+KHGL+ VVDNTF S
Sbjct: 130 FTFVDLNDAQALKAALKPNTKMIWAETPTNPMLKLVDLAKVAAFAKKHGLILVVDNTFCS 189

Query: 191 PMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFD 250
           PM+QRP   GADLV+HSATKYLNGHSDMVGGI VV    ELAE+M FLQNS+G V GPFD
Sbjct: 190 PMIQRPFESGADLVLHSATKYLNGHSDMVGGI-VVAREQELAERMGFLQNSVGAVAGPFD 248

Query: 251 SFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFG 310
           SFLA+RGLKTL LRM+AHCE+AL LAQWLE HP +E+VIYPGL SHPQH LA+RQM GFG
Sbjct: 249 SFLAMRGLKTLHLRMKAHCESALELAQWLEKHPEVERVIYPGLKSHPQHALARRQMHGFG 308

Query: 311 GIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISD 370
           GI+SI +KGG   A+R  E+  LF LAESLGGVESL+ HPA+MTHAS+P A R++LGISD
Sbjct: 309 GIISIEVKGGLRKARRMLERCHLFALAESLGGVESLIEHPAIMTHASVPPANRKRLGISD 368

Query: 371 ALVRLSVGIEDLGDLRGDLERAL 393
           +L+RLSVG+ED+ DLR +L  AL
Sbjct: 369 SLIRLSVGVEDIADLRSELAEAL 391


Lambda     K      H
   0.320    0.134    0.391 

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: 572
Number of extensions: 21
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: 397
Length of database: 392
Length adjustment: 31
Effective length of query: 366
Effective length of database: 361
Effective search space:   132126
Effective search space used:   132126
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, 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