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

GapMind for Amino acid biosynthesis

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_4305
          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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis