GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metB in Echinicola vietnamensis KMM 6221, DSM 17526

Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate Echvi_4510 Echvi_4510 Cystathionine beta-lyases/cystathionine gamma-synthases

Query= BRENDA::Q1M0P5
         (380 letters)



>FitnessBrowser__Cola:Echvi_4510
          Length = 403

 Score =  284 bits (727), Expect = 3e-81
 Identities = 163/392 (41%), Positives = 235/392 (59%), Gaps = 23/392 (5%)

Query: 4   QTKLIHGGISEDATTGAVSVPIYQTSTYRQDA------IGHHKG--YEYSRSGNPTRFAL 55
           QT+ IH G   D  TGA S  +  ++TY  +A       GH +   + Y+R GNPT   L
Sbjct: 12  QTRAIHAGELPDPVTGASSPNLVMSTTYLAEAGTGFSVEGHDEEDPWIYTRWGNPTVHQL 71

Query: 56  EELIADLEGGVKGFAFASGLAGIHAVF-SLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGL 114
           EE +A LE      AFASG+  I  +F  LL++GDH ++ D  Y     + N+++    +
Sbjct: 72  EEKLAVLEEAETAVAFASGMGAITVLFFHLLKAGDHAIVSDVAYAALSEMTNEMVPSLNI 131

Query: 115 SCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFA 174
             T +DTSDLS +K A+K NT+ +Y+ETP NP+L++TD+   A +A+  G    VD+TFA
Sbjct: 132 QITKVDTSDLSAVKAAVKNNTRLIYIETPCNPILRLTDIEAVAGIARGAGARLAVDSTFA 191

Query: 175 TPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQD 234
           TP    PL LGAD +VHS TKYLGGH D + G +      LA         +G V+ P +
Sbjct: 192 TPAATKPLQLGADFIVHSLTKYLGGHGDALGGAILGRKADLAPLRKKTAIRMGAVISPFN 251

Query: 235 SWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFS 294
           +WL+ RG+ T  +RM+AH+KNAL VA FLEKHPKV+RV YPGLP+HP +ELAKKQM+ FS
Sbjct: 252 AWLILRGLATFPIRMRAHEKNALKVAAFLEKHPKVKRVIYPGLPSHPQHELAKKQMKNFS 311

Query: 295 GMLSFTLKNDSEATP-FVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIR- 352
           GML+F ++N  + +  F + L++     SLG   SL+    ++  A + ++  + A  + 
Sbjct: 312 GMLTFQVENGKKRSGIFADKLRIVHYAVSLGHHRSLI---FYLDSADLKESSFKFATGKQ 368

Query: 353 ---------DGLVRLSVGIEHEQDLLEDLEQA 375
                    DG+ RLSVG+E  +D+++DL +A
Sbjct: 369 DESWEIYAGDGIFRLSVGLEDSKDIIDDLNRA 400


Lambda     K      H
   0.318    0.136    0.394 

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: 403
Number of extensions: 23
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: 380
Length of database: 403
Length adjustment: 31
Effective length of query: 349
Effective length of database: 372
Effective search space:   129828
Effective search space used:   129828
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