GapMind for Amino acid biosynthesis

 

Aligments for a candidate for CGL in Desulfovibrio vulgaris Miyazaki F

Align L-cysteine desulfidase (EC 4.4.1.28) (characterized)
to candidate 8501944 DvMF_2658 cysteine synthase (RefSeq)

Query= BRENDA::F4K5T2
         (323 letters)



>lcl|FitnessBrowser__Miya:8501944 DvMF_2658 cysteine synthase
           (RefSeq)
          Length = 310

 Score =  331 bits (849), Expect = 1e-95
 Identities = 165/304 (54%), Positives = 219/304 (72%), Gaps = 1/304 (0%)

Query: 7   IKNDVTELIGNTPMVYLNKIVDGCVARIAAKLEMMEPCSSIKDRIAYSMIKDAEDKGLIT 66
           I  D+TEL+G TP+V LN++ +GC A + AKLE   PC+S+KDRIA +MI  A ++G + 
Sbjct: 3   IARDMTELVGRTPLVRLNRVSEGCAAEVVAKLEFNNPCASVKDRIALAMIDGAMERGELA 62

Query: 67  PGKSTLIEATGGNTGIGLASIGASRGYKVILLMPSTMSLERRIILRALGAEVHLTDISIG 126
           PG   L+E T GNTG+GLA + A RG  ++L MP +MS ER+ +LR  GA + LT  S G
Sbjct: 63  PG-GLLVEPTSGNTGVGLAFVAAVRGLTLVLTMPESMSNERKALLRGFGARLVLTPASKG 121

Query: 127 IKGQLEKAKEILSKTPGGYIPHQFINPENPEIHYRTTGPEIWRDSAGKVDILVAGVGTGG 186
           ++G +E+A+ I+++TPG  +  QF+NP+NP +H +TT  EIW D+ GKVD  VAGVGTGG
Sbjct: 122 MRGAIEEAERIVAETPGAVMLGQFVNPDNPLVHRKTTAEEIWADTDGKVDAFVAGVGTGG 181

Query: 187 TVTGTGKFLKEKNKDIKVCVVEPSESAVLSGGKPGPHLIQGIGSGEIPANLDLSIVDEII 246
           TVTGTG+ L+E N DIKV  VEP ES VLSGG PGPH IQGIG+G +P  LD  + DEII
Sbjct: 182 TVTGTGRRLRELNPDIKVFAVEPDESPVLSGGAPGPHPIQGIGAGFVPPVLDTKVYDEII 241

Query: 247 QVTGEEAIETTKLLAIKEGLLVGISSGASAAAALKVAKRPENVGKLIVVIFPSGGERYLS 306
           +V G++A+ T + L  +EG+L G+SSGA+A AA+ VA+RPE  GK +V +    GERYLS
Sbjct: 242 RVPGKDALVTARRLLREEGILCGVSSGANAFAAMAVARRPEMAGKRVVFVVCDTGERYLS 301

Query: 307 TELF 310
           T LF
Sbjct: 302 TPLF 305


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: 278
Number of extensions: 8
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: 310
Length adjustment: 27
Effective length of query: 296
Effective length of database: 283
Effective search space:    83768
Effective search space used:    83768
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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