GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Phyllobacterium endophyticum PEPV15

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_106717515.1 CU100_RS15595 acetolactate synthase large subunit

Query= curated2:P37251
         (574 letters)



>NCBI__GCF_003010935.1:WP_106717515.1
          Length = 548

 Score =  254 bits (648), Expect = 8e-72
 Identities = 159/523 (30%), Positives = 272/523 (52%), Gaps = 19/523 (3%)

Query: 20  GALMLIESLKKEKVEMIFGYPGGAVLPIYDKLYNSGLVHILPRHEQGAIHAAEGYARVSG 79
           G+ +L+ +L+ E  + IFG PG   L + + + NS +  IL RHEQ A   A  Y R++G
Sbjct: 4   GSDLLVAALENEGTDRIFGIPGEENLDVVESIRNSSIQLILTRHEQAAAFMAATYGRLTG 63

Query: 80  KPGVVIATSGPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSDAFQEADILGITMPVT 139
           KPGV + T GPGA NL TG A A++ ++P+++ TGQ          FQ  D++    P+T
Sbjct: 64  KPGVCLTTLGPGALNLSTGAAYALLGAMPMIMITGQKGILSSRQARFQIVDVVASMKPLT 123

Query: 140 KHSYQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGEFSYDHEMNLPGYQPT 199
           K S Q+  P  +P +++EAF +A   RPGPV +++P+D+A  E E   +  +  P     
Sbjct: 124 KLSRQIVSPLMIPTMVREAFRVAQEERPGPVHLELPEDIAAEECE---NVALIAPHPVDL 180

Query: 200 TEPNYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQIPVAHTLLGLGGFP 259
              +   + +  E +  A++P+++ GA     +++ +L  +  + +IP   T +G G  P
Sbjct: 181 ATASDQALDRAAEIILRARRPLLMLGAAASRPRSTSDLAQFVLRTRIPFFTTQMGKGTVP 240

Query: 260 ADHPLFLGMAGMHGTYTANMALHECDLLISIGARFDDRVTGNLKHFARNAKIAHIDIDPA 319
               L++G A +      + A+ + DL+I+IG   D              K+ H+   PA
Sbjct: 241 GGTELYMGTAALSERDYVHEAIEQADLIITIG--HDTIEKPPFLMGEGGPKVVHVGYQPA 298

Query: 320 EIGKIMKTQIPVVGDSKIVLQELIKQ-DGKQSDSS---EWKKQLAEWKEEYPLWYVDNEE 375
            + ++   Q  VVGD    L+ L  + +GK +++      +K++ E             E
Sbjct: 299 SVEQVYFPQCEVVGDIGPSLKALADRIEGKLTNADALLHLRKRILE------RIGARATE 352

Query: 376 EGFKPQKLIEYIHQFTKGEAIVATDVGQHQMWSAQFYPFQKADKWVTSGGLGTMGFGLPA 435
           + F PQ+L+  + +    + I+A D G +++W A+ Y  + A+  +    L TMG GLP+
Sbjct: 353 DRFTPQRLVRAVREVMPHDGILALDNGMYKIWFARNYRTEMANTLLLDNALATMGAGLPS 412

Query: 436 AIGAQLAEKDATVVAVVGDGGFQMTLQELDVIRELNLPVKVVILNNACLGMVRQWQEIFY 495
           A+ A +      V+A+ GDGGF M  QEL+    L L + V+++ +   GM+R  Q +  
Sbjct: 413 AMTAAMLYPGRRVMAICGDGGFMMNSQELETAVRLKLNLVVLVIEDKAYGMIRWKQAV-- 470

Query: 496 EERYSESKFA-SQPDFVKLSEAYGIKGIRISSEAEAKEKLEEA 537
            +R+ +     + PDFVK +++Y  KG R+S   + K+ LE+A
Sbjct: 471 -DRFPDFGMTFNNPDFVKYAQSYAAKGTRVSDIGDFKDVLEKA 512


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: 664
Number of extensions: 32
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: 548
Length adjustment: 36
Effective length of query: 538
Effective length of database: 512
Effective search space:   275456
Effective search space used:   275456
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