GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Lentibacillus jeotgali Grbi

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_010531796.1 ON01_RS14505 sulfoacetaldehyde acetyltransferase

Query= metacyc::MONOMER-18810
         (585 letters)



>NCBI__GCF_000224785.1:WP_010531796.1
          Length = 590

 Score =  243 bits (620), Expect = 2e-68
 Identities = 176/554 (31%), Positives = 277/554 (50%), Gaps = 17/554 (3%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           +M  +E +V  L  E ++ V+G  G A + + D L        I VRHEQ+A H AD Y 
Sbjct: 17  KMTPSEAIVETLVAENIKEVYGIVGSAFMDMLD-LFPAAGIRFIPVRHEQSAGHMADAYE 75

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R +G  GV +  +GPG+TN VT +A A     P+VVI+ +  T+AIG D FQE + V I 
Sbjct: 76  RVSGTAGVIVGQNGPGITNMVTSVAAANQAHSPLVVISPSAGTNAIGMDGFQEANQVSIF 135

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           + I K    V +   +A  ++ AF IA   R GPV+ DIP+D+     +    +    R+
Sbjct: 136 KDITKETVQVTNKNRVADKLRTAFRIAYAER-GPVLFDIPRDLFYGEVEDVILEPHQYRA 194

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
            +    G    I  AV LL+ A+ P I +G G V A   D + ++A     P     M  
Sbjct: 195 -DKRGVGDPASIEHAVELLKNAKNPAIISGRGSVDAEGVDSVVKIAEYLTAPGATAYMHN 253

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGAR---FDDRVIGNPAHFTSQARKI 314
            AFP      VG +G  G   A  ++Q  DV++A+G R   F      +  +F + A KI
Sbjct: 254 DAFPADHPLAVGPIGYMGAKSAMYSLQEADVVLAVGTRLSQFGTLPCYDIDYFPTHA-KI 312

Query: 315 IHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKR-----EALAKWWEQIE 369
           I IDI+P  I +   V++ I+G+ K    E+  Q+K +   P++     +A+ K  E+ E
Sbjct: 313 IQIDINPRQIGRTHPVEVGIIGDAKAASDEIYRQLKLAMPSPEKDNERIQAVTKRKEEWE 372

Query: 370 QWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWI 429
           Q   VD    D   + I P+  + ++      +A + SD+G     A  + KF++ RR I
Sbjct: 373 Q-ELVDSAMED--GDPINPRRALLEMTRAMPENAIVSSDIGNVSSTANAYLKFNQTRRHI 429

Query: 430 NSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNN 489
            +   G  G   P A+G + A P+  V  I G+G+  M + E+ST ++ + PV  C  NN
Sbjct: 430 AALTFGNTGFAYPAALGAQLAEPDAPVFAIVGDGAWGMSLHEVSTAVEQNIPVIACVFNN 489

Query: 490 GYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLK 549
                 ++ Q   YD+RY  S + A P+F ++A++ G +G  ++K  D+ PA+ +  + +
Sbjct: 490 KAWAAEKKNQVDYYDDRYVGSDIKA-PEFAEVAKSMGALGYTIDKPEDIGPAIEDVLKQR 548

Query: 550 DRTVFLDFQTDPTE 563
              V L+   D T+
Sbjct: 549 KPAV-LNIYVDGTQ 561


Lambda     K      H
   0.319    0.135    0.407 

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: 772
Number of extensions: 43
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: 585
Length of database: 590
Length adjustment: 37
Effective length of query: 548
Effective length of database: 553
Effective search space:   303044
Effective search space used:   303044
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