GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Desulfovibrio vulgaris Hildenborough

Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate 206250 DVU0823 arginine biosynthesis bifunctional protein ArgJ

Query= SwissProt::Q9Z4S1
         (397 letters)



>MicrobesOnline__882:206250
          Length = 393

 Score =  283 bits (725), Expect = 5e-81
 Identities = 171/397 (43%), Positives = 236/397 (59%), Gaps = 11/397 (2%)

Query: 4   PRGFSYAGVHCRIKRK-RKDLGIIFSEVPCTAAGVFTTNVVKAAPVIYDMEILGKNPSGI 62
           P+GF +A V    +++ R DL +I S+ P TAAGVFTTN  +AAPV+   E L   P   
Sbjct: 5   PKGFRFATVSAGFRKEARPDLALIVSDTPATAAGVFTTNRFQAAPVVVARENLSARPVA- 63

Query: 63  RAITVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKVESG 122
           RA+ +NSG ANACTG++GM N R   +   K   IP   VL +STGVIG QL M+K    
Sbjct: 64  RAVVINSGQANACTGDEGMTNCRTTLDLVGKACGIPAAEVLPASTGVIGAQLHMDKWREA 123

Query: 123 IEEAVKNLSKDPV-PFAEAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNMATM 181
                  L ++    FA AIMTTD   K+  +++ I G  + ++G+AKG+GMI PNMATM
Sbjct: 124 APRLAAALGQNTHHDFARAIMTTDAFPKVAERELAIAGTTVRLVGMAKGAGMICPNMATM 183

Query: 182 LSFITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAGNAPIQEETD 241
           LS +  DA V+ +A ++L   +VD ++N + VDGDTSTND V  LANG +G   +  E +
Sbjct: 184 LSVVLCDAAVTPEAWQRLFLDAVDRTFNRVTVDGDTSTNDTVFGLANGASG---VTVEGE 240

Query: 242 GFWKLYEAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSNLVKTA 301
              KL EA+ +V   LA  +V+DGEGATKV+ V+V  A D   A  +AR +  S LVKTA
Sbjct: 241 DLAKLGEALTDVLARLAYMLVQDGEGATKVMRVKVSGAVDDAEAEAVARTVGHSQLVKTA 300

Query: 302 IYGEDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFDEDT-AKKILS 360
           +YG DANWGR++AA G SGA F  + + +   +  G +++  NGQ  D D DT  ++ L 
Sbjct: 301 MYGRDANWGRIVAAVGRSGASFKAEDVVV---TLCG-VELFRNGQPTDLDFDTLLREPLK 356

Query: 361 EKKVKIILDMKQGKELARAWGCDLTEKYVEINGRYRT 397
            + V + +++  G         DLT  YV  N  YR+
Sbjct: 357 GRDVTVDIELGAGTGHYELLASDLTHDYVNCNADYRS 393


Lambda     K      H
   0.315    0.133    0.371 

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: 371
Number of extensions: 19
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: 397
Length of database: 393
Length adjustment: 31
Effective length of query: 366
Effective length of database: 362
Effective search space:   132492
Effective search space used:   132492
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 (21.6 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