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_085635546.1 MGEO_RS04765 thiamine pyrophosphate-binding protein

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_002115805.1:WP_085635546.1
          Length = 550

 Score =  264 bits (675), Expect = 6e-75
 Identities = 164/535 (30%), Positives = 262/535 (48%), Gaps = 13/535 (2%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALY--DGGVEHLLCRHEQGAAMAAIGYA 58
           +  A  +V  L AQG    FG PG + +PV DA Y  +  +  + CR E GAAM A  Y 
Sbjct: 8   IRAADLLVDQLVAQGTTAAFGVPGESYLPVLDAFYGRESDIRFVTCRQEGGAAMMADAYG 67

Query: 59  RATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLS 118
           + TG+ G+C AT GPGATN   G+  A  DS P++   GQV+   +  +AFQE+D   + 
Sbjct: 68  KLTGRPGICFATRGPGATNASAGVHVAFQDSTPMILFLGQVARDMLDREAFQEIDYRRMF 127

Query: 119 LACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENE 178
               K    +     L   ++ AF  A SGRPGPV++ +P+D+             VE  
Sbjct: 128 GQMAKWVAQIDDASRLQEYVSRAFRTAMSGRPGPVVLALPEDMLYDEIPRPKPPARVETP 187

Query: 179 VTFP-HAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAV 237
              P HA +   R  +A+A+ P++  GGG   ++ + AL+ F     +P + +L+  G +
Sbjct: 188 RFGPGHAALNAIRDRIAQAKSPLVMAGGGGWTSKGIAALQTFAETQGLPVSVSLRCQGLM 247

Query: 238 EADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVT---GKLNTFAPHASVIHMD 294
           +  +P Y+G  G+         + E DL IA+G R  +  T     L+   P+ S+IH+ 
Sbjct: 248 DNRHPNYIGHYGVGTPPYLKDIMAETDLFIAIGPRLGEMTTAGYSLLSPPVPNLSLIHVF 307

Query: 295 IDPAEMNKLRQAHVALQGDLNALLPALQ--QPLNQYDWQQHCAQLRDEHSWRYDHPGDAI 352
            +P E+ ++ +  +A+  D  +   A+   +P+    +     +LR ++   +  P    
Sbjct: 308 PEPEELGRVFEPEIAVAADTESFCEAVADWEPITPGTFTDRTTELRKQYE-TFSDPASVS 366

Query: 353 YAPL--LLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAA 410
             PL  L   L+   P + +V    G +  W  +   +  P + +  +  G+MG+GLPAA
Sbjct: 367 GDPLAPLFAHLAGVLPENAIVCNGAGNYAAWLHRFYCYRAPGSQLAPTS-GSMGYGLPAA 425

Query: 411 VGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQ 470
           +GA +  P+  +  I+GDG FMM  QE+ T     L L +++++N R G +R  Q+  + 
Sbjct: 426 IGAAICEPDREIFAIAGDGCFMMTCQEMATAAHHGLNLTVIIINNARYGTIRAHQEREYP 485

Query: 471 ERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSID 525
           +R S T LT NPDF   A +FG H +     D+  A L       G  L+ V  D
Sbjct: 486 DRVSGTALT-NPDFCDFARSFGAHAERAGDIDRFAAVLAAARERGGLNLIEVPAD 539


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: 736
Number of extensions: 34
Number of successful extensions: 7
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: 550
Length adjustment: 36
Effective length of query: 512
Effective length of database: 514
Effective search space:   263168
Effective search space used:   263168
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: 53 (25.0 bits)

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

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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