GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CGL in Cupriavidus basilensis 4G11

Align L-cysteine desulfidase (EC 4.4.1.28) (characterized)
to candidate RR42_RS21960 RR42_RS21960 cysteine synthase

Query= BRENDA::F4K5T2
         (323 letters)



>FitnessBrowser__Cup4G11:RR42_RS21960
          Length = 305

 Score =  251 bits (642), Expect = 1e-71
 Identities = 142/303 (46%), Positives = 194/303 (64%), Gaps = 5/303 (1%)

Query: 9   NDVTELIGNTPMVYLNKIVDGCVARIAAKLEMMEPCSSIKDRIAYSMIKDAEDKGLITPG 68
           +++ + IGNTP + + ++  G   ++  K E   P  SIKDRIA SM++ AE  G++ PG
Sbjct: 4   DNILQTIGNTPHIRVQRLF-GDTHQVWIKSERANPGGSIKDRIALSMVEAAEQSGVLKPG 62

Query: 69  KSTLIEATGGNTGIGLASIGASRGYKVILLMPSTMSLERRIILRALGAEVHLTDISIGIK 128
             T+IE T GNTGIGLA + A +GYK++L+MP +MS+ERR ++ A GA   LT    G+K
Sbjct: 63  -GTIIEPTSGNTGIGLAMVAAVKGYKLVLVMPDSMSVERRRLMLAYGATFDLTPREKGMK 121

Query: 129 GQLEKAKEILSKTPGGYIPHQFINPENPEIHYRTTGPEIWRDSAGKVDILVAGVGTGGTV 188
           G + +A+E+++ TPG ++P QF NP N E H  TT  EI  D    +D LV GVGTGG +
Sbjct: 122 GAIARAEELVAATPGAWMPQQFENPANIEAHVNTTALEILADFPQGIDALVTGVGTGGHI 181

Query: 189 TGTGKFLKEKNKDIKVCVVEPSESAVLSGGKPGPHLIQGIGSGEIPANLDLSIVDEIIQV 248
           TG  + LK+K   +KV  VEP  S V+SGG P PH IQGIG+G IP NLD +++D +IQV
Sbjct: 182 TGCARVLKQKWPALKVYAVEPVASPVISGGAPAPHPIQGIGAGFIPRNLDTALLDGVIQV 241

Query: 249 TGEEAIETTKLLAIKEGLLVGISSGAS-AAAALKVAKRPENVGKLIVVIFPSGGERYLST 307
             E A E  +  A +EG+LVGISSGA+ AA A K+   P   G  ++      GERYL+ 
Sbjct: 242 DAEPAREMARRAAREEGMLVGISSGATLAAIAQKLPDLP--AGATVLGFNYDTGERYLTV 299

Query: 308 ELF 310
           E F
Sbjct: 300 EGF 302


Lambda     K      H
   0.314    0.136    0.378 

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: 280
Number of extensions: 13
Number of successful extensions: 2
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: 323
Length of database: 305
Length adjustment: 27
Effective length of query: 296
Effective length of database: 278
Effective search space:    82288
Effective search space used:    82288
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: 42 (21.9 bits)
S2: 48 (23.1 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