GapMind for Amino acid biosynthesis

 

Alignments 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)



>MicrobesOnline__882:408370
          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:

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