GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Desulfovibrio vulgaris Hildenborough

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 209104 DVU0171 hemolysin-related protein

Query= SwissProt::Q08432
         (387 letters)



>MicrobesOnline__882:209104
          Length = 393

 Score =  299 bits (765), Expect = 1e-85
 Identities = 155/387 (40%), Positives = 222/387 (57%), Gaps = 4/387 (1%)

Query: 3   FDKREERLGTQSVKWDKTGELFGVT--DALPMWVADMDFRAPEAITEALKERLDHGIFGY 60
           FD   +R GT S+KWD    +FG    +A+P+WVADMDF APEA+  A+K+    GI+GY
Sbjct: 9   FDTLIDRTGTGSLKWDDMERIFGPVPQNAIPLWVADMDFHAPEAVQNAVKDVAAQGIYGY 68

Query: 61  TTPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYT 120
                  ++A   W+ +RHGW    ES+   PGVV  +++ ++  T PGD V VQPPVY 
Sbjct: 69  PAESSAPREAAATWLADRHGWAPGKESLVTVPGVVPGMALLIRELTAPGDGVAVQPPVYP 128

Query: 121 PFYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWSRE 180
           P +  V   GR ++ NPL+E DG + +D   LE  +    V L +LC+PHNP GR W+R+
Sbjct: 129 PLFDCVRAAGRRVVENPLVETDGRWGMDLGGLEG-IFKGGVRLLLLCSPHNPVGRVWTRD 187

Query: 181 DLLKLGELCLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTCAAPSKTFNIAG 240
           +L  L +LC  +GV VV+DEIH DL+L GH HT FASL     D  VTC + SK+FN+ G
Sbjct: 188 ELSALADLCQRYGVMVVADEIHHDLVLPGHTHTVFASLPQCQPDRVVTCVSASKSFNLGG 247

Query: 241 LQASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLDELITYIEKNMN 300
           L  + ++  D   R + + ++   GL   + F + A EAA+  G PWLD L  YI  N  
Sbjct: 248 LPHAYVVATDGALRQRIAHAVVGRGLAHGDLFGMVAQEAAHRHGAPWLDALRMYIADNAA 307

Query: 301 EAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYGPGG 360
             +  L + LP V+M   + +YL WLD  A G+ +  + +R++  G V+   G  +G GG
Sbjct: 308 MLQDRLHSHLPWVRMATLEGTYLAWLDCRASGMDETTMMRRLVAAG-VVPSGGRFFGTGG 366

Query: 361 EGFMRLNAGCSLATLQDGLRRIKAALS 387
           EG +R+N       L   + R+   L+
Sbjct: 367 EGHLRVNLATPRTRLSAAIARMIVGLA 393


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: 442
Number of extensions: 20
Number of successful extensions: 4
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: 393
Length adjustment: 31
Effective length of query: 356
Effective length of database: 362
Effective search space:   128872
Effective search space used:   128872
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 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 (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:

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. 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:

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:

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