GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Streptacidiphilus oryzae TH49

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_037577100.1 BS73_RS27900 thiamine pyrophosphate-requiring protein

Query= curated2:O08353
         (599 letters)



>NCBI__GCF_000744815.1:WP_037577100.1
          Length = 600

 Score =  238 bits (608), Expect = 4e-67
 Identities = 178/573 (31%), Positives = 278/573 (48%), Gaps = 34/573 (5%)

Query: 4   AEAMIKALEAEKVEILFGYPGGALLPFYDALHHS--DLIHLLTRHEQAAAHAADGYARAS 61
           ++ +++ L    V+ +FGYPG  +     A   +      +  RHE+ AA  A GYA+ S
Sbjct: 6   SDFILRRLREWDVDYVFGYPGDGINGLLSAWERAGDQPRFIQARHEEMAAFEAVGYAKFS 65

Query: 62  GKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPI 121
           G+VGVC  TSGPGA +L+ G+  A  D  P+VAL GQ     IG    QE+D   L+  +
Sbjct: 66  GRVGVCAATSGPGAIHLLNGLYDAKLDHVPVVALVGQTAQTAIGGSYQQEVDLPNLYKDV 125

Query: 122 VKHNFQIQKTC-QIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180
                Q+  T  Q+P +   A  IAQ  R     + +P DVQ+LE     H        +
Sbjct: 126 ASEYCQLVTTPEQLPNVLDRAMRIAQ-ARKTVTAVIVPADVQDLEYSAPTHAFKMVPSSL 184

Query: 181 GYNPTT-IGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLM 239
           G++ +  + H   + +A +++ S  +  ILAG G    GA+ EL++  E+L   V   L+
Sbjct: 185 GFSGSAYVPHEDDLARAAEVLNSGSKVAILAGQGA--RGASAELIETAEVLGAGVAKALL 242

Query: 240 GKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIH 299
           GK  + ++ P   G  G+ GT+P    + + D L+ IG  F    +  +  F   A+ + 
Sbjct: 243 GKDVLPDDLPFVTGASGLLGTRPTYELMKDCDTLLVIGSSFP--YSQFLPEFG-QARAVQ 299

Query: 300 IDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSL 359
           IDIDP  IG     +V +VGDA+  L+ ++  L    ++  +E  ++ N S+W E +   
Sbjct: 300 IDIDPGRIGMRYPFEVNLVGDARETLRRLLPLLSRKEDRGWREKIEQNN-SRWWEVMK-- 356

Query: 360 KKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPR 419
           +++S+     +  PI P+  V     V+D L +    IIT D G    W A + + +   
Sbjct: 357 RRASV-----EADPINPEYAVH----VLDGL-LPGRAIITADSGSAANWYARHLRIREGI 406

Query: 420 SFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMN-CQELGTIAEY-----NI 473
           +   SG L TMG G P AIGAK + PD   I + GDG   MN   EL T+ +Y     + 
Sbjct: 407 NGSLSGTLATMGPGVPYAIGAKFSCPDRPAIALVGDGAMQMNGLAELITVGKYWQEWRDP 466

Query: 474 PVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPD--FIKLAESYGIKARRIESPNEI 531
            +V+C+ +N+ L  V  W+          +     PD  +   A   G+   R+E P E+
Sbjct: 467 RLVVCVLNNQDLNQV-TWEMRSMSGSPQFLPSQQLPDVRYADFARGLGLHGIRVEKPEEV 525

Query: 532 NEALKEAINCDEPYLLDFAIDPSSALSMVPPGA 564
             A + A+  D P +LD   DP  A+  +PP A
Sbjct: 526 EPAWRAALESDRPCVLDVLTDP--AVPPIPPHA 556


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: 799
Number of extensions: 46
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: 600
Length adjustment: 37
Effective length of query: 562
Effective length of database: 563
Effective search space:   316406
Effective search space used:   316406
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