Alignments for a candidate for metC in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for metC in Dinoroseobacter shibae DFL-12

Align Cystathionine beta-lyase PatB; CBL; Beta-cystathionase PatB; Cysteine lyase PatB; Cysteine-S-conjugate beta-lyase PatB; EC 4.4.1.13 (characterized)
to candidate 3606747 Dshi_0178 aminotransferase class I and II (RefSeq)

Query= SwissProt::Q08432
         (387 letters)



>FitnessBrowser__Dino:3606747
          Length = 390

 Score =  253 bits (647), Expect = 5e-72
 Identities = 145/397 (36%), Positives = 207/397 (52%), Gaps = 20/397 (5%)

Query: 1   MNFDKREERLGTQSVKWDKTGELFGVT--DALPMWVADMDFRAPEAITEALKERLDHGIF 58
           M FD   +R  T  +KWDK    FGV+  D L MW+ADMDF     + EA++  L    +
Sbjct: 1   MTFDTEIDRRNTDCIKWDKMESAFGVSPEDGLAMWIADMDFPPGPFLQEAMQGLLARADY 60

Query: 59  GYTTPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPV 118
           GY    +  +DA+ GWM++RHGW V  E +  + G+   +++ + A T PGD+V++  PV
Sbjct: 61  GYFCGLESYEDAIIGWMRDRHGWTVEREWMFTTYGLGNGIAITLNALTAPGDEVIIFSPV 120

Query: 119 YTPFYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWS 178
           Y  F   + K GR +   PL   DG Y +DF+     LS    T+ I C+PHNP+GR W+
Sbjct: 121 YHEFAAKITKTGRVVKELPLAIVDGVYTMDFDAYAGMLSGRE-TMVIACSPHNPAGRVWT 179

Query: 179 REDLLKLGELCLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTCAAPSKTFNI 238
           +E+L  L + C  H + ++SDEIH+DL   GH H P    +   AD  V   + SKTFNI
Sbjct: 180 QEELTALADFCQRHDLLLISDEIHADLTFAGHTHIPMHVAAPQIADRLVMTTSASKTFNI 239

Query: 239 AGLQASAIIIPDRLKRAKF-----SASLQRNGLGGLNAFAVTAIEAAYS-KGGPWLDELI 292
           AG +   + IPD   RA+F     +  +Q N LG      V    AAYS  G  W D L 
Sbjct: 240 AGGRTGCVTIPDPDLRARFHRFFNTLDMQPNLLG------VALTRAAYSPAGAAWCDALC 293

Query: 293 TYIEKNMNEAEAFLS--TELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVIL 350
           TY+E N   A  F      +P +  M    +YL W+DF+  G+   E  +R+    ++  
Sbjct: 294 TYLEGN---AAVFNDGVNAIPGLSAMPMQGTYLAWVDFAGTGMERPEFSERVYGTARIAA 350

Query: 351 EPGTKYGPGGEGFMRLNAGCSLATLQDGLRRIKAALS 387
            PG   G GGE  +R N G   A +Q+ + R+  A +
Sbjct: 351 TPGHTLGKGGESCLRFNVGMPRARVQEAVDRLADAFA 387


Lambda     K      H
   0.318    0.135    0.408 

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: 491
Number of extensions: 31
Number of successful extensions: 5
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: 387
Length of database: 390
Length adjustment: 30
Effective length of query: 357
Effective length of database: 360
Effective search space:   128520
Effective search space used:   128520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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