GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CGL in Echinicola vietnamensis KMM 6221, DSM 17526

Align L-cysteine desulfidase (EC 4.4.1.28) (characterized)
to candidate Echvi_0220 Echvi_0220 cysteine synthase B

Query= BRENDA::F4K5T2
         (323 letters)



>FitnessBrowser__Cola:Echvi_0220
          Length = 292

 Score =  198 bits (504), Expect = 1e-55
 Identities = 121/298 (40%), Positives = 179/298 (60%), Gaps = 11/298 (3%)

Query: 13  ELIGNTPMVYLNKIVDGCVARIAAKLEMMEPCSSIKDRIAYSMIKDAEDKGLITPGKSTL 72
           ELIGNTP+V L  I      +I  KLE   P  S+KDR AYSMIK A D+G +  G   +
Sbjct: 5   ELIGNTPLVELEHIPTNPNVKIYCKLEGQNPGGSVKDRAAYSMIKRAMDRGDLKQG-DRV 63

Query: 73  IEATGGNTGIGLASIGASRGYKVILLMPSTMSLERRIILRALGAEVHLTDISIGIKGQLE 132
           +EAT GNTGI LA I    G ++ L+MP   + ER + + A GA+V LT  +  I+    
Sbjct: 64  VEATSGNTGIALAMIAKVLGVEMTLIMPDNSTRERVVSMEAYGAKVILTPAAKTIEYSRT 123

Query: 133 KAKEILSKTPGGYIPHQFINPENPEIHYRTTGPEIWRDSAGKVDILVAGVGTGGTVTGTG 192
            A+E ++K  G YI +QF NP+N + HY  TGPEI RD+ G++   V+ +GT GT+ G  
Sbjct: 124 LAEE-MAKNEGYYILNQFANPDNYQAHYEGTGPEIMRDTNGEITHFVSAMGTTGTIMGVS 182

Query: 193 KFLKEKNKDIKVCVVEPSESAVLSGGKPGPHLIQGIGSGEIPANLDLSIVDEIIQVTGEE 252
           ++LKE+   +++   +P++ + + G       I+      +P   D S VD+II V+ EE
Sbjct: 183 RYLKEQKPAVQIVGTQPTDGSSIPG-------IRRWSPEFLPKIYDASRVDQIIDVSQEE 235

Query: 253 AIETTKLLAIKEGLLVGISSGASAAAALKVAKRPENVGKLIVVIFPSGGERYLSTELF 310
           A E T+ +A +EG+L G+SSG +  AA+K+A+  ++   +IV I    G+RYLS++LF
Sbjct: 236 ATEMTRRMAKEEGILAGMSSGGALHAAVKLAESLDS--GVIVCITCDRGDRYLSSDLF 291


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: 243
Number of extensions: 15
Number of successful extensions: 5
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: 292
Length adjustment: 27
Effective length of query: 296
Effective length of database: 265
Effective search space:    78440
Effective search space used:    78440
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