GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Azorhizobium caulinodans ORS 571

Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_012170314.1 AZC_RS09265 citramalate synthase

Query= curated2:Q8TYB1
         (499 letters)



>NCBI__GCF_000010525.1:WP_012170314.1
          Length = 537

 Score =  215 bits (548), Expect = 3e-60
 Identities = 167/517 (32%), Positives = 254/517 (49%), Gaps = 29/517 (5%)

Query: 3   DRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIA 62
           +R+ +FDTTLRDG QT GV  T+ +K+ +   L+  GVD +EAG+P A+  + +      
Sbjct: 10  ERLYLFDTTLRDGAQTNGVDFTLADKLNVIGLLNRLGVDYVEAGYPGANPTDTQLFAQKR 69

Query: 63  GEELDAEICGLA----RCVKGD--IDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALE 116
                    G+     R V  D  + A + A+ D +      S   +R  LE + EE L 
Sbjct: 70  PSAARVTAFGMTKRAGRSVSNDPGVAALLAAEADAICFVAKASAFQVRVALETTEEENLA 129

Query: 117 RAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMTP 173
              E V  A   G       E   D  + + D+ L   +A  +AGA  V + DT G   P
Sbjct: 130 SIRESVAAAVAAGREALVDCEHFFDGFKENPDFALACAEAAYQAGARWVVLCDTNGGTLP 189

Query: 174 PEMYRLTAEVVDAVDVP-VSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGNAS 232
            E+  + A V   V    V +H HND   AVANSLAAV AGA Q+  T+NG+GER GNA+
Sbjct: 190 HEVEAIVARVTARVPGSHVGIHAHNDTEQAVANSLAAVRAGARQIQGTLNGLGERCGNAN 249

Query: 233 LEQVVMALKALYD----IELDVRTEMLVEL---SRLVERLTGVVVPPNTPIVGENAFAHE 285
           L  ++  L    D     E  V  E L E+   SR ++ +       + P VGE+AFA +
Sbjct: 250 LCSLIPTLLLKGDYAERFETGVSREALAEIGVVSRTLDEMLNRSPDRHAPYVGESAFATK 309

Query: 286 SGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEV--TEEQLDE 343
           +GIH+  ++K   TYE + PE VG++RR+++   AGR  +  +LE +G+ V   + +L  
Sbjct: 310 AGIHASAILKDPATYEHVPPEAVGNQRRVLVSDQAGRSNVLAELERLGVPVDRADPRLAR 369

Query: 344 IVRRVKELGDKG--KRVTEDDLEAIARDVVGEVPE----SEAAVKLEEIAVMTGNKFT-P 396
           ++  VKE    G      +     +AR ++  VP+       +VK+E      G   T  
Sbjct: 370 LLDEVKEREALGYAYEAADASFALLARRMLHSVPDFFTVERFSVKVERRYNAKGEMTTVA 429

Query: 397 TASVRVYLDGEEHEAASTGVGSVDAAIRALREAI---EELGMDVELKEYRLEAITGGTDA 453
            A V+V +  E   +A+ G G V+A   ALR+ +   +     + L +YR+  + GGT+A
Sbjct: 430 EAIVKVRVGDEVFISAAEGNGPVNALDVALRKDLGKYQPYIAGLRLTDYRVRILNGGTEA 489

Query: 454 LAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFVRGV 490
           +  V V   DE G   T  G + +I+ AS +A +  +
Sbjct: 490 VTRVLVESTDESGARWTTVGVSPNIIDASFEALLDSI 526


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: 553
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: 537
Length adjustment: 35
Effective length of query: 464
Effective length of database: 502
Effective search space:   232928
Effective search space used:   232928
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 25 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