GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Steroidobacter denitrificans DSM 18526

Align cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_066917961.1 ACG33_RS00985 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase

Query= BRENDA::P43623
         (340 letters)



>NCBI__GCF_001579945.1:WP_066917961.1
          Length = 424

 Score =  122 bits (306), Expect = 2e-32
 Identities = 94/316 (29%), Positives = 150/316 (47%), Gaps = 37/316 (11%)

Query: 53  GRFYGTAGSPTIDNLENAWTHLTGGAGTVLSASGLGSISLALLALSKAGDHILMTDSVYV 112
           G  Y    +PT D LE     L GG G++  ++G+ ++  A++ L++AGD+I+    +Y 
Sbjct: 49  GNIYTRIMNPTCDVLEKRVAMLEGGVGSLALSAGMAAVHYAIINLAEAGDNIVSVPQLYG 108

Query: 113 PTRMLCDGLLAKFGVETDYYDPSIGKDIEKLVKPNTTVIFLESPGSGTMEVQDIPALVSV 172
            T  L   +L K G+ET +        IEKL+   T  IF ES G+    + D+ A+  +
Sbjct: 109 GTYTLFAHMLPKMGIETRFAADDSAAAIEKLIDAKTKAIFFESIGNPAGNIVDVEAVAKM 168

Query: 173 AKKHGIKTILDNTWATPLFFDAHAHGIDISVEAGTKYLGGHSDLLIGLA--------SAN 224
           A+ HG+ TI+DNT ATP       +GIDI V A TKY+GGH   L GL         + +
Sbjct: 169 ARGHGVATIVDNTVATPSLLKPIDYGIDIVVHALTKYMGGHGTTLGGLIVDSGNFPWADH 228

Query: 225 EECWPLLRSTYDAM-------AMLPGAE-------------------DCQLALRGMRTLH 258
           ++ +P+     +A        A+ P A                    +    L+G+ TL 
Sbjct: 229 QQRYPMFNEPEEAYHGVVYVDALGPAAYIGRARTVPLRNTGAALSPFNAFQLLQGIETLP 288

Query: 259 LRLKEVERKALDLAAWLGNRDEVEKVLHPAFEDCPGHEYWVRDYKG-SSGLFSIVLKNGF 317
           LR++     A  +A  L     VE V +   ++ P H    +  KG +SG+ +  +K GF
Sbjct: 289 LRMERHCENAQRVAEHLQEHAMVEWVSYAGLKNHPHHALAQKYMKGRASGILTFGVKGGF 348

Query: 318 TRAGLEKMVEGMKVLQ 333
             AG+ K  + +K+ +
Sbjct: 349 D-AGV-KFYDALKLFK 362


Lambda     K      H
   0.318    0.137    0.411 

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: 354
Number of extensions: 21
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 340
Length of database: 424
Length adjustment: 30
Effective length of query: 310
Effective length of database: 394
Effective search space:   122140
Effective search space used:   122140
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 Apr 10 2024. The underlying query database was built on Apr 09 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