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_1734 Echvi_1734 Cystathionine beta-lyases/cystathionine gamma-synthases

Query= BRENDA::Q1M0P5
         (380 letters)



>FitnessBrowser__Cola:Echvi_1734
          Length = 369

 Score =  310 bits (794), Expect = 4e-89
 Identities = 177/381 (46%), Positives = 236/381 (61%), Gaps = 15/381 (3%)

Query: 1   MHMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYEYSRSGNPTRFALEELIA 60
           M  +T  IHGG  + A   AV  PI  ++T+      H +   YSRS NP R ALEEL+A
Sbjct: 1   MKFETLAIHGGEKKSAPHRAVVQPITLSTTFEH----HEESLIYSRSQNPNRMALEELLA 56

Query: 61  DLEGGVKGFAFASGLAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGLSCTIID 120
            LE G    AF+SG A   AVF  L  G H++   D+Y G  +   + L K+ L  T  D
Sbjct: 57  QLEKGSAAAAFSSGNAAGMAVFQALPLGSHIVAPSDMYHGLKKQLVE-LFKDKLEVTFTD 115

Query: 121 TSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQN 180
            SD   ++KAI+PNTK L++ETPSNP+LKI+D+ +   +AK+  +  + DNTFATP +QN
Sbjct: 116 LSDPENLEKAIQPNTKLLWIETPSNPMLKISDIRRLTKMAKEDDIRVVCDNTFATPVFQN 175

Query: 181 PLLLGADIVVHSGTKYLGGHSDVVAG-LVTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQ 239
           PL LGAD+V+HS TKY GGHSD++ G L+T  ++   ++I   Q   G VL P D +LL 
Sbjct: 176 PLELGADLVMHSATKYFGGHSDILGGALITKKSDEFWKQIVNVQQTGGAVLSPFDCYLLV 235

Query: 240 RGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSF 299
           R IKTL  RM+ H ++A  +A FL++HPKVERV+YPGL  HP +++AK QM GF G+LSF
Sbjct: 236 RSIKTLAYRMRGHAEHAGMIATFLDQHPKVERVFYPGLTAHPGHDVAKSQMTGFGGILSF 295

Query: 300 TLKNDSE-ATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLVRL 358
            +K   E A   + SLK +    SLGGVESL+   A +     P T+         L+RL
Sbjct: 296 LVKGKPEDADKLISSLKYYTNATSLGGVESLIERRAAVEG---PDTKTP-----QNLIRL 347

Query: 359 SVGIEHEQDLLEDLEQAFAKI 379
           SVG+EH  DLLED+E+AF  I
Sbjct: 348 SVGLEHLDDLLEDMEKAFYSI 368


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: 411
Number of extensions: 15
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: 369
Length adjustment: 30
Effective length of query: 350
Effective length of database: 339
Effective search space:   118650
Effective search space used:   118650
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