GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Ruegeria conchae TW15

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_010443520.1 G7G_RS0121375 thiamine pyrophosphate-binding protein

Query= curated2:O08353
         (599 letters)



>NCBI__GCF_000192475.1:WP_010443520.1
          Length = 593

 Score =  296 bits (758), Expect = 2e-84
 Identities = 185/570 (32%), Positives = 292/570 (51%), Gaps = 44/570 (7%)

Query: 4   AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASGK 63
           AE ++  LE  +V+ +FG  G   +    AL  S +  +  RHEQ A+HAAD YAR + K
Sbjct: 12  AEHIVDFLERREVKHVFGLCGHTNIAVLAALAESPIDFVTVRHEQIASHAADAYARVTDK 71

Query: 64  VGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALG------L 117
             V +    PG TN  TGVA A  D  PMV + G +PT   G    QE++         +
Sbjct: 72  ASVVLSHLSPGLTNCATGVANAALDCIPMVVIAGDIPTHYYGKHPHQEVNLHADAAQWEI 131

Query: 118 FMPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPS-K 176
           + P VK  +++ +   + EI   AF +A++G+PGPV +++P       +DI    IPS  
Sbjct: 132 YRPFVKRAWRVDRADLMAEILEKAFHLAESGQPGPVLVNVP-------MDIFSEVIPSDS 184

Query: 177 VKLIGYNPTTIGHP----RQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNI 232
              I  N   +  P       ++ ++ +A A+ P+   GGG+LL+ A+EEL + VE + +
Sbjct: 185 FDRIRDNTRALKKPSIDDESAREIVEALAKAENPVAYVGGGILLAQASEELREFVEHMGL 244

Query: 233 PVCTTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSF- 291
           PV  +LMGKG + ++HPL LGM G  GT+  N     +D + ++G RF +    D  S+ 
Sbjct: 245 PVAHSLMGKGALRDDHPLVLGMTGFWGTELVNQSCLNADYIFAVGTRFKE---ADCSSWY 301

Query: 292 ------ATNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENND 345
                    +K+IHIDI+P EIG+N   ++ +V DAK  L+     L+ +  +   +   
Sbjct: 302 PGYTFNIPGSKVIHIDIEPQEIGRNYPTEIGVVADAKAALRV----LNRVAREMYPDGFK 357

Query: 346 KENISQWIENVNS-LKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQ 404
           +  + Q I +  +  K  ++ +      P+ P++I+ +    + +     + IITTDVG 
Sbjct: 358 RPALEQKIADFRTDFKARNLEMAISSAFPMMPERILADTRKALPE-----DAIITTDVGW 412

Query: 405 NQMWMAHYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQE 464
           N+  +   F   TP S L+ GG  TMGFG P AIGAK+A PD  V+ + GDGGF  N   
Sbjct: 413 NKNGVGQQFDILTPGSILTPGGFATMGFGPPGAIGAKLAAPDRVVLSLVGDGGFGQNPSM 472

Query: 465 LGTIAEYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGA------PDFIKLAESY 518
           L T  E ++ ++  + +N   G +   Q   YG    +   G A      P +  +A +Y
Sbjct: 473 LATAVELDLGIIWLVMNNNAFGTIAGLQKAHYGLTYGTTFPGSAEAPANGPGYADIARAY 532

Query: 519 GIKARRIESPNEINEALKEAINCDEPYLLD 548
           G +  R+ + +E+  AL+ AI   +P +LD
Sbjct: 533 GAEGHRLSAADELLPALEAAIASGKPTVLD 562


Lambda     K      H
   0.319    0.137    0.405 

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: 860
Number of extensions: 40
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: 599
Length of database: 593
Length adjustment: 37
Effective length of query: 562
Effective length of database: 556
Effective search space:   312472
Effective search space used:   312472
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 (21.7 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