GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Lentibacillus jeotgali Grbi

Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS; Vegetative protein 105; VEG105 (uncharacterized)
to candidate WP_029328972.1 ON01_RS03645 acetolactate synthase

Query= curated2:P37251
         (574 letters)



>NCBI__GCF_000224785.1:WP_029328972.1
          Length = 545

 Score =  298 bits (764), Expect = 3e-85
 Identities = 180/538 (33%), Positives = 281/538 (52%), Gaps = 10/538 (1%)

Query: 18  MSGALMLIESLKKEKVEMIFGYPGGAVLPIYDKLYNSGLVHILP-RHEQGAIHAAEGYAR 76
           M+ A  ++E +K E +   F  PG + LP+ D LY+   + ++  RHE GA   A+GYA+
Sbjct: 1   MTAAQAIVECMKTEGISDAFCVPGESYLPLMDALYDESSIRLISARHESGAAFMADGYAK 60

Query: 77  VSGKPGVVIATSGPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSDAFQEADILGITM 136
            S KPGVV+AT G GA+NL  G+  A  DS P++VF GQV +   G + FQE D+     
Sbjct: 61  SSLKPGVVMATRGVGASNLSIGVHTAYQDSTPMIVFLGQVHSKFRGREGFQEIDLEQYFR 120

Query: 137 PVTKHSYQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGEFSYDHEMNLPGY 196
              K + +V+ PE +  I++ AF IA TGRPGPV++ +P+DV   E E ++      P  
Sbjct: 121 HTAKWAVEVKAPERVAEIVQRAFRIAQTGRPGPVVVSLPEDVLPAEAEMTF----GPPAV 176

Query: 197 QPTTEPNYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQIPVAHTLLGLG 256
           +P   P   +I+ + E +++++KP+I+AG GV   +A + L ++AE+  +PV        
Sbjct: 177 KPKPVPAQEEIKLVEELLATSEKPLIIAGGGVKTSEAEDALVSFAEKYSLPVIAAFRRQD 236

Query: 257 GFPADHPLFLGMAGMHGTYTANMALHECDLLISIGARFDDRVTGNLKHFARNAKIAHIDI 316
            FP +H L+ G  G+         + E   +++IG R  +  T + +  A   K+ HIDI
Sbjct: 237 VFPNNHRLYAGHLGLGTNANILQTVKEAGTILAIGTRLSEVTTQDYQILAPEKKLIHIDI 296

Query: 317 DPAEIGKIMKTQIPVVGDSKIVLQELIKQDGKQSDSSEWKKQLAEWKEEYPLWYVDNEEE 376
               IGK+    I +V D+K  L+ L + + K +  S W        EE     V +++ 
Sbjct: 297 SYDVIGKVYSPDIGIVADAKKALKALERMEIKSTWKS-WVNSRRRAFEEISSLGVSHKDA 355

Query: 377 GFKPQKLIEYIHQFTKGEAIVATDVGQHQMWSAQFYPFQKADKWVTSGGLGTMGFGLPAA 436
             K   ++  +       A+V  D G    W   FYPF+    +V     G MG+GLP A
Sbjct: 356 INK--HIVSVMAGMLPDNALVTNDAGNFAGWLHAFYPFKGKHTYVGPTS-GAMGYGLPGA 412

Query: 437 IGAQLAEKDATVVAVVGDGGFQMTLQELDVIRELNLPVKVVILNNACLGMVRQWQEIFYE 496
           +GA+LA  D  V+A+ GDGGF MT+QEL+      +PV  ++ NN   G +R  QE+ Y 
Sbjct: 413 LGAKLALPDKPVIALAGDGGFMMTMQELETAVRYKIPVISLVFNNDMYGTIRMHQEMHYP 472

Query: 497 ERYSESKFASQPDFVKLSEAYGIKGIRISSEAEAKEKLEEALTSREPVVIDVRVASEE 554
           E+   +    +  F  L+E+ G +G  + S  E  E  + AL +  P VI++    E+
Sbjct: 473 EKVIGTDL-GRISFKNLAESVGAEGYLVKSADEFSEAFDAALQNNVPAVIEIMTEKEQ 529


Lambda     K      H
   0.317    0.135    0.391 

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: 809
Number of extensions: 45
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: 574
Length of database: 545
Length adjustment: 36
Effective length of query: 538
Effective length of database: 509
Effective search space:   273842
Effective search space used:   273842
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: 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