GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CGL in Phaeobacter inhibens BS107

Align L-cysteine desulfidase (EC 4.4.1.28) (characterized)
to candidate GFF1378 PGA1_c13950 cysteine synthase CysK

Query= BRENDA::F4K5T2
         (323 letters)



>FitnessBrowser__Phaeo:GFF1378
          Length = 344

 Score =  179 bits (453), Expect = 1e-49
 Identities = 119/329 (36%), Positives = 177/329 (53%), Gaps = 18/329 (5%)

Query: 7   IKNDVTELIGNTPMVYLNKIVDGCVARIAAKLEMMEPCSSIKDRIAYSMIKDAEDKGLIT 66
           I +D+ + IG+TP++ LN++ D     I  K E M P  S+KDR A  +IKDA  +G + 
Sbjct: 3   IAHDLADAIGHTPLIRLNRVSDETGCEILGKAEFMNPGQSVKDRAALYIIKDAIARGDLK 62

Query: 67  PGKSTLIEATGGNTGIGLASIGASRGYKVILLMPSTMSLERRIILRALGAEV------HL 120
           PG  T++E T GNTGIGLA +GAS G+K ++++P T S E++ +LR  GA++        
Sbjct: 63  PG-GTIVEGTAGNTGIGLALVGASMGFKTVIVIPETQSEEKKDMLRLAGAQLVQVPAAPY 121

Query: 121 TDISIGIKGQLEKAKEILSKTPGGYI-PHQFINPENPEIHYRTTGPEIWRDSAGKVDILV 179
            + +  ++     AKE+    P G I  +QF N  N + H  TT PEIW  + GKVD  V
Sbjct: 122 RNPNNFVRYSERLAKELAKTEPNGAIWANQFDNVANRQAHVETTAPEIWEQTGGKVDGFV 181

Query: 180 AGVGTGGTVTGTGKFLKEKNKDIKVCVVEPSESAVLSG------GKPGPHLIQGIGSGEI 233
             VG+GGT+ G    L+ K   +K+ + +P  +A+ S          G  + +GIG   I
Sbjct: 182 CAVGSGGTLAGVADALQPKG--VKIGLADPMGAALYSYYTTGEIATEGGSIAEGIGQVRI 239

Query: 234 PANLDLSIVDEIIQVTGEEAIETTKLLAIKEGLLVGISSGASAAAALKVAKRPENVGKLI 293
             NL+    D   Q+   +A+     L  +EGL++G SS  + A A+++AK     GK I
Sbjct: 240 TKNLEGFKPDFCYQIEDRDALPYVFDLLHEEGLVLGGSSAINIAGAVRMAK-DMGPGKTI 298

Query: 294 VVIFPSGGERYLSTELFESVRYEAENLPV 322
           V +    G RY S +LF       +NLPV
Sbjct: 299 VTVLCDYGTRYQS-KLFNPDFLREKNLPV 326


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: 300
Number of extensions: 18
Number of successful extensions: 4
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: 344
Length adjustment: 28
Effective length of query: 295
Effective length of database: 316
Effective search space:    93220
Effective search space used:    93220
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: 49 (23.5 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