GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Sphingomonas indica Dd16

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_085218094.1 B9N75_RS06660 cystathionine gamma-synthase family protein

Query= BRENDA::Q5H4T8
         (397 letters)



>NCBI__GCF_900177405.1:WP_085218094.1
          Length = 434

 Score =  217 bits (552), Expect = 6e-61
 Identities = 147/410 (35%), Positives = 212/410 (51%), Gaps = 29/410 (7%)

Query: 11  GDRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSS---------------PGEHQG 55
           G R L  ATL +  G  P  S G++  PI+ TST+   +               PG  +G
Sbjct: 24  GGRKLKPATLMMGHGFDPALSEGSLKAPIFLTSTFVFENAAAGKRHFEGVTGKRPGGAEG 83

Query: 56  FEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVM-ELLDAGSHVVAMDDLYGG 114
             YSR + P +   E  +AA E    +  F+SGM+A +T++   +  G  +V    LY  
Sbjct: 84  LVYSRFNGPNQEILEDRLAAWEDAEDSLTFSSGMSAIATLLLTFVQPGDVIVHSGPLYAA 143

Query: 115 TFRLFERVRRR--TAGLDF---SFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIA 169
           T  L  R+  R     LDF   +  D       KA  +    ++++E+P NP   LVD+ 
Sbjct: 144 TETLIGRILGRFGVTWLDFPAGATGDEISAVLEKAKAQGRVSLIYLESPANPTNALVDVE 203

Query: 170 AIA-----VIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAV 224
           A+A     V          +DNTF  P+  +PL  GADL V+S TKY  GHSD+V G  +
Sbjct: 204 AVAASRDAVFGGDEKPPIAIDNTFLGPLWSKPLEHGADLSVYSLTKYAGGHSDLVAG-GI 262

Query: 225 VGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPA 284
           VG  A L + +  ++N+IG +  P  +++ LR L+TL LRM    ENA  +  +   HP 
Sbjct: 263 VGSKA-LLDPIRMMRNTIGTITDPNTAWMLLRSLETLELRMSRAGENAEKVCAFFRDHPK 321

Query: 285 IEKVIYPG-LASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGV 343
           +E V Y G L    Q  + +R  +G G   S+ LKGG   A  F +  ++  LA SLGG 
Sbjct: 322 VESVGYLGFLKDGRQADIYRRHCTGAGSTFSLYLKGGEREAFAFLDALKIAKLAVSLGGT 381

Query: 344 ESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393
           E+L + PA MTH S+P  R++ LGI+D LVR+S+G+ED  DL  D ++AL
Sbjct: 382 ETLASAPAAMTHLSVPDERKQALGITDNLVRISIGVEDADDLIADFDQAL 431


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: 466
Number of extensions: 25
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: 434
Length adjustment: 31
Effective length of query: 366
Effective length of database: 403
Effective search space:   147498
Effective search space used:   147498
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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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