GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CGL in Cupriavidus basilensis 4G11

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate RR42_RS06465 RR42_RS06465 O-acetylhomoserine aminocarboxypropyltransferase

Query= BRENDA::Q5H4T8
         (397 letters)



>FitnessBrowser__Cup4G11:RR42_RS06465
          Length = 436

 Score =  263 bits (672), Expect = 7e-75
 Identities = 163/416 (39%), Positives = 224/416 (53%), Gaps = 42/416 (10%)

Query: 19  TLAIHGGQSPDPSTGAVMPPIYATSTY--------AQSSPGEHQGFEYSRTHNPTRFAYE 70
           TLA+H G +PDP+TGA   PI+ T+++        A     E  G  YSR  NPT    E
Sbjct: 8   TLALHAGAAPDPATGARATPIHLTTSFVFKDSEHAASLFNMERAGHVYSRISNPTVAVLE 67

Query: 71  RCVAALEGGTRAFAFASGMAATS-TVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGL 129
             +AALE G  A   ASG AA    V  L+ AGSH+VA   LYGG+  L     RR  G+
Sbjct: 68  ERIAALENGAGAIGVASGQAALHLAVATLMGAGSHIVASSALYGGSHNLLHYTLRRF-GI 126

Query: 130 DFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFA 189
           + +FV   D  A++AAIR +TK+++ ET  NP L ++DI  +A + + +G+  +VD+TF 
Sbjct: 127 ETTFVQARDIDAWRAAIRPETKLLFGETLGNPGLDVLDIPTLAQLGQDNGIPLLVDSTFT 186

Query: 190 SPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDN---------AELAEQMAFLQN 240
           +P L +P  LGA L+ HSATK+L GH   +GG+   G            EL+E  A   N
Sbjct: 187 TPYLLKPFDLGAGLLYHSATKFLGGHGTTIGGVLAEGGTFDFEASGRFPELSEPYAGFHN 246

Query: 241 SI----------------------GGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQW 278
            +                      G    P  ++  L+G++TLPLRM  H +NA  + Q+
Sbjct: 247 MVFTEESTVAPFLLRARREGLRDFGACLSPMAAWQLLQGIETLPLRMARHVDNARRVVQF 306

Query: 279 LETHPAIEKVIYPGLASHPQHVLAKRQM-SGFGGIVSIVLKGGFDAAKRFCEKTELFTLA 337
           L +HP +E V YP L SHP + LA+R +  G G + S  LKG   A +RF E   LF+  
Sbjct: 307 LVSHPMVESVAYPELESHPDYALARRLLPRGAGAVFSFNLKGNRAAGQRFIESLALFSHL 366

Query: 338 ESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393
            ++G   SLV HPA  TH  +  A  +  GIS+  +RLSVG+ED  DL  DL+R L
Sbjct: 367 ANVGDARSLVIHPASTTHFRMDAAALQAAGISEGTIRLSVGLEDPDDLIDDLKRGL 422


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: 481
Number of extensions: 24
Number of successful extensions: 6
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: 436
Length adjustment: 31
Effective length of query: 366
Effective length of database: 405
Effective search space:   148230
Effective search space used:   148230
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