GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Streptacidiphilus oryzae TH49

Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_037572568.1 BS73_RS14685 citramalate synthase

Query= curated2:Q8TYB1
         (499 letters)



>NCBI__GCF_000744815.1:WP_037572568.1
          Length = 533

 Score =  209 bits (532), Expect = 2e-58
 Identities = 162/511 (31%), Positives = 252/511 (49%), Gaps = 31/511 (6%)

Query: 3   DRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIA 62
           D   +FDTTLRDG Q  G+ LTV +K+ IAR LDEFGV  IE G+P A+  + E     A
Sbjct: 8   DAFHVFDTTLRDGAQREGIKLTVADKLTIARHLDEFGVGFIEGGWPGANPRDTEFFSR-A 66

Query: 63  GEELDAEIC-----GLARCVKG------DIDAAIDADVDCVHVFIATSDIHLRYKLEMSR 111
             ELD         G  R   G       + A +D+    V +   + D H+   L  + 
Sbjct: 67  ATELDLSHAQLVAFGSTRRANGTAAEDQQLKALLDSGAPVVTLVAKSHDRHVELALRTTL 126

Query: 112 EEALERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTV 168
           +E L    + VE+    G  V    E   D  R +R+Y L V +   EAGAD V + DT 
Sbjct: 127 DENLAMVRDSVEFLRAQGRRVFIDCEHYFDGYRANREYALSVVRTAHEAGADVVVLCDTN 186

Query: 169 GVMTPPEMYRLTAEVVDAVDVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERA 228
           G M P  +  + A+ +      + +H  +D G AVAN+LAAVE GA  V  T NG GER 
Sbjct: 187 GGMLPSGVREIVADTLAETGARLGIHAQDDTGCAVANTLAAVEGGATHVQCTANGYGERV 246

Query: 229 GNASLEQVVMALKALYDIELDVRTEMLVELSRLVERLTGVV-VPPNT--PIVGENAFAHE 285
           GNA+L  V  AL+      + +    L E++R+   +  VV + P T  P VG +AFAH+
Sbjct: 247 GNANLFPVTAALELKLGRSV-LPAGRLAEMTRISHAIAEVVNLAPATHQPYVGVSAFAHK 305

Query: 286 SGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVT--EEQLDE 343
            G+H+  +    + Y+ I PE VG+  R+++   AGR +++ K +E+G +++   E +  
Sbjct: 306 GGLHASAIKVDPDLYQHIDPELVGNTMRMLVSDMAGRASVELKGKELGFDLSGDRELVGR 365

Query: 344 IVRRVKELGDKG--KRVTEDDLEAIARDVVGEVPESEAAVKLEEIAV--MTGNKFTPTAS 399
           +V  +KE  + G      +   E + R+  G++P+   A++     V      +    A+
Sbjct: 366 VVDVLKERENAGYTYEAADASFELLLREQSGDLPQRFFALESWRAIVEQRPDGEQANEAT 425

Query: 400 VRVYLDGEEHEAASTGVGSVDAAIRALREAIEELGMDV---ELKEYRLEAI--TGGTDAL 454
           V+++  GE       G G V+A  RALR  +E +   +   EL +Y++  +    GT+++
Sbjct: 426 VKLWAKGERLVTTGEGNGPVNALDRALRAGLERIYPQLAAFELVDYKVRILEERHGTESV 485

Query: 455 AEVTVRLEDEDGNVTTARGAAEDIVMASVKA 485
             V V   D     +T  G   +++ AS +A
Sbjct: 486 TRVLVTTSDGKSEWSTV-GVGSNVIAASWQA 515


Lambda     K      H
   0.315    0.133    0.364 

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: 571
Number of extensions: 26
Number of successful extensions: 4
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: 499
Length of database: 533
Length adjustment: 35
Effective length of query: 464
Effective length of database: 498
Effective search space:   231072
Effective search space used:   231072
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 (21.5 bits)
S2: 52 (24.6 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