GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hcs in Desulfovibrio vulgaris Hildenborough

Align Homocitrate synthase 1; EC 2.3.3.14 (uncharacterized)
to candidate 408370 DVUA0016 homocitrate synthase

Query= curated2:Q44290
         (377 letters)



>lcl|MicrobesOnline__882:408370 DVUA0016 homocitrate synthase
          Length = 384

 Score =  201 bits (512), Expect = 2e-56
 Identities = 132/363 (36%), Positives = 190/363 (52%), Gaps = 6/363 (1%)

Query: 4   VLINDTTLRDGEQAAGVVFTLEEKVAIAKFLDTIGVPELEVGIPAMGEEEMRAICAI-SN 62
           V++ D+TLR+G QA GV F   ++ +I + +   GV E E G    G++++ A   + + 
Sbjct: 22  VMLIDSTLREGAQAYGVYFDAADRESILQGVAASGVTEAEAGWA--GQDDLAATLRLGAR 79

Query: 63  LGLKANLLAWNRAVISDIKASVACGMERVHIAIPVSGIQIAAKFHGQWRVSLQRLKDCIS 122
           +     L  W R   +D+  +   G  RVHI +P S   +  +        LQR+   + 
Sbjct: 80  VAPSLRLAVWCRCCTADLDKAAEAGARRVHIGVPSSDAHMRLRLGMGRDEVLQRVTTVLE 139

Query: 123 FAVDQG-LWVAVGGEDSSRADENFLLDVALYAQEWGASRFRFCDTVGVLDPFTTYGKVKL 181
            A   G L V +G ED+ RA  + L  +A  A   GA R R  DTVG+L P      V L
Sbjct: 140 HAAHLGFLHVTLGLEDAGRAAPDLLEALARTAARTGAHRLRCSDTVGLLTPDGMVRLVLL 199

Query: 182 LVSALTIPVEVHTHNDFGMATANALAGIKAGASSVNTTVIGLGERAGNAALEEVVMAIKR 241
              A  +PV VH HND G+ATANALA + AGA   + +++GLGERAG    EE+  A+  
Sbjct: 200 ARRASALPVAVHCHNDLGLATANALAALDAGADGADVSLLGLGERAGITRAEELAAALVV 259

Query: 242 IYGVDMGIDTPRLLELSQLVAAASGANVPPWKAIVGENTFAHESGIHAHGVLQNPDTYEP 301
           + G    +D   L  + + +AA+    +PP  A+ GEN FA ESG+H HGV ++P  +EP
Sbjct: 260 LRGESYRLD--MLRGVCRRLAASLEMRLPPHWAVAGENLFAVESGVHLHGVQRDPALFEP 317

Query: 302 FAPEEVGWERRLVVGKHSGRHSVSNLLEQHGIFLNPEETQSVLDAVRQQSIKKKRSLTTE 361
           F P  VG ERRL VG   G   V+ +   HG+ L  +  +  + AVR ++    R LT  
Sbjct: 318 FPPALVGAERRLGVGGKCGSAGVAAMAHSHGLTLQGDALRRHVRAVRDKACSLGRPLTDA 377

Query: 362 ELL 364
           E L
Sbjct: 378 EFL 380


Lambda     K      H
   0.318    0.133    0.388 

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: 382
Number of extensions: 17
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: 377
Length of database: 384
Length adjustment: 30
Effective length of query: 347
Effective length of database: 354
Effective search space:   122838
Effective search space used:   122838
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 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 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