GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Streptacidiphilus oryzae TH49

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_051940866.1 BS73_RS27520 dihydroxy-acid dehydratase

Query= BRENDA::A0A481UJA7
         (614 letters)



>NCBI__GCF_000744815.1:WP_051940866.1
          Length = 572

 Score =  320 bits (820), Expect = 1e-91
 Identities = 192/468 (41%), Positives = 275/468 (58%), Gaps = 24/468 (5%)

Query: 135 GVSDAISMGTRGMCYSLQSRDLIADSIETVMSAQWYDGNISIPGCDKNMPGTIMAMGRLN 194
           G+SD    GT  M YSL  R+   D I   +      G I++  CDK   GT+ A+   N
Sbjct: 67  GISDGQRNGTPQMRYSLIGRETTNDGICLHLEGSDVRGAIAVVACDKPPVGTLAALLERN 126

Query: 195 RPSIMVYGGTIKPG--HYNGHSYDIISAFQAYGEYVNGSISDEDRKNVVHNSCPGAGACG 252
            P++++  G+I+PG     G   DII+ FQA       +   ++R+ V   + PG G+CG
Sbjct: 127 VPAVIMSDGSIRPGVDSRTGERIDIITCFQA------AAAEPDERRRVALEASPGHGSCG 180

Query: 253 GMYTANTMASAIEAMGMCLPYSSSIPAENPLKLDECRLAGKYLLELL-KMDLKPQNIITP 311
           GM+T NTM S I   GM   +  S  +E+P ++ E       +L+LL +  ++P++I+TP
Sbjct: 181 GMFTYNTMQSFIATCGMEPLHMVSPASEDPRRIKEFPGQLLDVLQLLTERGIRPRDIVTP 240

Query: 312 QSLRNAMVVVMALGGSTNAVLHLIPIARSVGLE-----LTLEDFQKVSDEVPFLADLKPS 366
            +LRNA +V +A+GGSTN VLH   +AR+ G++     ++ ++F ++S  +P L +  P 
Sbjct: 241 AALRNATLVAIAMGGSTNVVLHAPELARAAGIDFWREVISQDEFNRMSRRLPVLVNAWPF 300

Query: 367 GKYVMEDVHKIGGTPAVLRYLLEHGFLDGDCLTVTGKTLAENVQNCPPLSEGQDIIRPLE 426
           G+Y M D+   GG P ++  LL  G LDG CLT TG+TLAE V    P +   D+I PL 
Sbjct: 301 GRYSMVDIDAKGGLPVIVNELLAAGMLDGSCLTCTGETLAEQVARLDPPAPDGDVIHPLS 360

Query: 427 NPIKKTGHIQILQGNLAPE-GSVAKI----TGKEGLYFSGPALVFEGEEAMLAAISENPM 481
            P K TG +++L+GNLAPE G+V K+    +G E   F G A VF+ E+A+L A++  P 
Sbjct: 361 APFKPTGGLRLLRGNLAPEGGAVIKLAGVESGMEDGRFVGRARVFDSEQALLDALTSAPE 420

Query: 482 NFKGK-VVVIRGEGPKGGPGMPEMLTPTSAI--MGAGLGKDCALLTDGRFSGGSHGFVVG 538
            F+ + +VVIR EGP+G PGMPEML PTS I  +    G   AL+TD RFSGGS G V+G
Sbjct: 421 EFQDRDMVVIRYEGPRGAPGMPEMLDPTSRITALCRQRGITIALMTDARFSGGSVGLVIG 480

Query: 539 HICPEAQEGGPIGLVRNGDIIRIDVRERRIDVDVTDQ--EMEERRKNW 584
           H+ PEA +GGPI L+ +GD I +DV +  +D    D     EERR  W
Sbjct: 481 HVSPEAAQGGPIALIEDGDTIVVDVNQDTLDCTELDDPATAEERRARW 528


Lambda     K      H
   0.316    0.135    0.401 

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: 889
Number of extensions: 50
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: 614
Length of database: 572
Length adjustment: 37
Effective length of query: 577
Effective length of database: 535
Effective search space:   308695
Effective search space used:   308695
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