GapMind for Amino acid biosynthesis

 

Aligments 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_2080 Echvi_2080 Cystathionine beta-lyases/cystathionine gamma-synthases

Query= BRENDA::Q1M0P5
         (380 letters)



>lcl|FitnessBrowser__Cola:Echvi_2080 Echvi_2080 Cystathionine
           beta-lyases/cystathionine gamma-synthases
          Length = 381

 Score =  395 bits (1014), Expect = e-114
 Identities = 197/381 (51%), Positives = 260/381 (68%), Gaps = 2/381 (0%)

Query: 1   MHMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYEYSRSGNPTRFALEELIA 60
           M   TK+IH G++ D TTGA+  PI+QTSTY Q + G HKG+EYSR+ NPTR AL++ IA
Sbjct: 1   MKFGTKVIHAGVAPDPTTGAIMTPIFQTSTYVQKSPGQHKGFEYSRTHNPTRDALQKSIA 60

Query: 61  DLEGGVKGFAFASGLAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGLSCTIID 120
            LE G  G  F+SG+  I A+  LL  GD V+  +D+YGGT+R+F KV  K G+    + 
Sbjct: 61  ALENGKHGLCFSSGMGAIDALIKLLSPGDEVISTNDLYGGTYRIFTKVFAKYGIKFHFVS 120

Query: 121 TSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQN 180
             D + I+K I   T+ ++ ETP+NP++ I D+   A++A  H LL  VDNTFATPY QN
Sbjct: 121 MDDPASIEKYINDKTRLIWAETPTNPMMNIIDIKALAAIAGKHDLLLGVDNTFATPYLQN 180

Query: 181 PLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQR 240
           PL LGAD+V+HS TKYL GHSDVV G +  N++ LA+++AF QN+ G   GPQD +L+ R
Sbjct: 181 PLDLGADLVMHSVTKYLAGHSDVVMGALVVNDDRLAEDLAFIQNSCGATPGPQDCFLVLR 240

Query: 241 GIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSFT 300
           GIKTL LRM+ H +N   +A +L  HPKV++VY+PG   HPN+++A KQMR F GM+SF+
Sbjct: 241 GIKTLHLRMERHCQNGKTIAGYLRHHPKVDKVYWPGFEDHPNHDIAAKQMRDFGGMISFS 300

Query: 301 LKND--SEATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLVRL 358
           +  D   +A   +E+L  F L ESLGGVESL G PA MTHA IPK +RE  G+ D L+RL
Sbjct: 301 IVGDKQEDAKKVLENLHYFSLAESLGGVESLCGHPASMTHASIPKVEREKVGLTDSLIRL 360

Query: 359 SVGIEHEQDLLEDLEQAFAKI 379
           SVG+E  +DL  DL  A   I
Sbjct: 361 SVGVEDAEDLKNDLAAALELI 381


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: 472
Number of extensions: 16
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: 380
Length of database: 381
Length adjustment: 30
Effective length of query: 350
Effective length of database: 351
Effective search space:   122850
Effective search space used:   122850
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 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