GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CGL in Dyella japonica UNC79MFTsu3.2

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate N515DRAFT_4363 N515DRAFT_4363 cystathionine gamma-synthase

Query= BRENDA::Q5H4T8
         (397 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4363
          Length = 399

 Score =  341 bits (875), Expect = 2e-98
 Identities = 182/378 (48%), Positives = 241/378 (63%), Gaps = 2/378 (0%)

Query: 16  SLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAA 75
           S +T A+  G   D   GAV+PP++ ++ YA    G  + ++YSR+ NPTR      +A 
Sbjct: 9   STSTCAVRAGIESDTQHGAVVPPLHLSTNYAFEGLGGKRAYDYSRSGNPTRDLLGNALAE 68

Query: 76  LEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVD 135
           LE G  A   ASGMAA +  +EL+ AG  V+A  D YGGT+RL +   ++       F D
Sbjct: 69  LEQGAGAVVTASGMAAVALALELVPAGGRVLAAHDCYGGTWRLLDAWAKK-GRFTLEFAD 127

Query: 136 LTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQR 195
           LTD  A  A + +   +VW+ETP+NP+L++ D+  +A  A   G L VVDNTF SP LQ+
Sbjct: 128 LTDRVALAAGLASKPSLVWVETPSNPLLRITDVRHVAQAAHAAGALVVVDNTFLSPALQQ 187

Query: 196 PLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLAL 255
           PL LGAD+VVHS TKY+NGHSD+VGG  V  D A +A+Q+ +  N  G    PFDSFL L
Sbjct: 188 PLVLGADVVVHSTTKYINGHSDVVGGAVVARDQA-VADQLKWWGNCNGLTGAPFDSFLTL 246

Query: 256 RGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSI 315
           RGL+TL +R+R H ENA  +A  L+ H A+ KV YPGL SHP H LA RQ +GFG ++S 
Sbjct: 247 RGLRTLSVRLRQHQENAQRIATLLDGHAAVRKVYYPGLESHPGHALAARQQAGFGAMLSF 306

Query: 316 VLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRL 375
            L+G     + F  + + F+LAESLGGVESLV HPA MTHAS+    R   GI+D+L+R+
Sbjct: 307 ELEGDVAQIEAFVNELKYFSLAESLGGVESLVAHPASMTHASMAPEARRTAGIADSLLRI 366

Query: 376 SVGIEDLGDLRGDLERAL 393
           SVGIED  DL  D++  L
Sbjct: 367 SVGIEDGDDLVRDVDAGL 384


Lambda     K      H
   0.320    0.134    0.391 

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: 477
Number of extensions: 20
Number of successful extensions: 3
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: 397
Length of database: 399
Length adjustment: 31
Effective length of query: 366
Effective length of database: 368
Effective search space:   134688
Effective search space used:   134688
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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