GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CGL in Magnetospirillum magneticum AMB-1

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_043745532.1 AMB_RS21365 O-succinylhomoserine sulfhydrylase

Query= BRENDA::Q5H4T8
         (397 letters)



>NCBI__GCF_000009985.1:WP_043745532.1
          Length = 403

 Score =  263 bits (672), Expect = 7e-75
 Identities = 154/362 (42%), Positives = 224/362 (61%), Gaps = 9/362 (2%)

Query: 39  IYATSTYAQSS-PGEHQGFEYSRTHNPTRFAYERCVAALEGG-----TRAFAFASGMAAT 92
           +Y ++  A++S  G      YSR  NPT   +E+ +A +EG        A A ASGMAA 
Sbjct: 42  VYDSAEEAEASFDGTLDRMVYSRFKNPTVAVFEQRLAEMEGAPPGMAVAARATASGMAAV 101

Query: 93  -STVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTK 151
            + ++  L AG  VVA   L+G    +   +  R  G++  FVD TD  +++AA+   T 
Sbjct: 102 HAALLCQLRAGDRVVASTALFGSCHWIINELLPRY-GVERVFVDGTDLKSWEAALSRPTA 160

Query: 152 MVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKY 211
            V++ETP+NP L+++D+AA+  +A K G   VVDN FA+P+LQ PL LGAD+VV+SATK+
Sbjct: 161 CVFLETPSNPTLEIIDLAAVCELAHKAGAKVVVDNVFATPILQSPLELGADIVVYSATKH 220

Query: 212 LNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCEN 271
           ++G    +GG AV+G     A+ +     + G    PF++++ L+GL+TL LRM  HC N
Sbjct: 221 MDGQGRCLGG-AVLGSPEFCADILGPFLRNTGPALSPFNAWVLLKGLETLDLRMERHCAN 279

Query: 272 ALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKT 331
           AL +A++LE  P + +V+YPGL SHPQH LAKRQM G+G IV++ LKGG  AA +     
Sbjct: 280 ALKVARFLEARPEVARVLYPGLESHPQHDLAKRQMRGWGSIVALELKGGKPAAYKLLNGV 339

Query: 332 ELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLER 391
           EL  ++ +LG  +SL+ HP   TH  +    +  +GI++ L+RLSVG+ED  DL  DL R
Sbjct: 340 ELIDISNNLGDAKSLITHPWTTTHQRLSPEDKLSMGITEGLLRLSVGLEDGDDLVEDLGR 399

Query: 392 AL 393
           AL
Sbjct: 400 AL 401


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: 457
Number of extensions: 18
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: 403
Length adjustment: 31
Effective length of query: 366
Effective length of database: 372
Effective search space:   136152
Effective search space used:   136152
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