GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Marivita geojedonensis DPG-138

Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate WP_085641493.1 MGEO_RS19930 5-guanidino-2-oxopentanoate decarboxylase

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_002115805.1:WP_085641493.1
          Length = 531

 Score =  194 bits (492), Expect = 9e-54
 Identities = 156/530 (29%), Positives = 235/530 (44%), Gaps = 19/530 (3%)

Query: 3   GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATG 62
           GAQ +   L+ +GV+T+FG PG   + +Y  +   G+ H+L RHEQGA   A GYARATG
Sbjct: 7   GAQ-ISQMLKERGVDTIFGIPGVHNVELYRGIEQAGITHVLARHEQGAGFMADGYARATG 65

Query: 63  KTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEV-DVLGLSLAC 121
           K GV    +GPG TN++T L  A  DS+PV+AI+  +           ++ D    +   
Sbjct: 66  KPGVAYVITGPGLTNILTPLGQAYSDSVPVLAISSCLDEVAARRGQLHQMRDQRMAAETV 125

Query: 122 TKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEV-T 180
              S   +S      ++  AFD   S R  P  + +  +   A  D  P        + +
Sbjct: 126 CAWSEEARSASAAYALIDRAFDQFASARARPCHMQVSIETLGALADPAPQPPAARPGLPS 185

Query: 181 FPHAEVEQARQMLAKAQKPMLYVGGG-VGMAQAVPALREFLAATKMPATCTLKGLGAVEA 239
             H++V      +  A+KP+   GGG V  A A+P   + L  T   +  T    G V A
Sbjct: 186 ASHSDVYDVVAAVLAAKKPLFVFGGGSVAAADAIP---DLLRQTGAASIVTYAARGVVPA 242

Query: 240 DYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAE 299
           D P Y G        A   A  + DL+IAVG    + V     T    A +I +DIDP  
Sbjct: 243 DEPLYFGSYLARPDSAEITA--QADLVIAVGTTLSE-VDLWRPTLGHTAPMIRVDIDPEV 299

Query: 300 MNKLRQAHVALQGDLNALLPAL------QQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIY 353
              +     A+  D  A L A+      +       W    +  R   +WR +   +   
Sbjct: 300 FTGMGPEDRAILADAGAFLKAMTIAIPARTDTKPPKWDA-ASVARKRAAWRAEVDAERPG 358

Query: 354 APLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGA 413
              +   L    P D ++ +D+ Q    A +     RP ++    G GT+G+ LPAA+G 
Sbjct: 359 IVPVCDALRAVLPDDTMIYSDMTQFAYAAKEIWDMPRPGHWHHPYGFGTLGYALPAAIGG 418

Query: 414 QVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERY 473
            VARP    + I+GD      +QELGT     LPL I++ DN +LG +     +   +  
Sbjct: 419 AVARPGLPTLAIAGDYGLQYTIQELGTAVELGLPLPILVWDNGKLGEIE--DSMVRSQIA 476

Query: 474 SETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVS 523
               +  NPDFL LA A+G         + ++ A+     +DGP ++ V+
Sbjct: 477 PNAVVARNPDFLALAKAYGAEAVQPDSLEALQQAMLAAFKADGPTVIRVT 526


Lambda     K      H
   0.320    0.135    0.410 

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: 713
Number of extensions: 38
Number of successful extensions: 6
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: 548
Length of database: 531
Length adjustment: 35
Effective length of query: 513
Effective length of database: 496
Effective search space:   254448
Effective search space used:   254448
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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