GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Sinorhizobium meliloti 1021

Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate SMc02546 SMc02546 alpha-isopropylmalate/homocitrate synthase family transferase

Query= curated2:Q8TYB1
         (499 letters)



>FitnessBrowser__Smeli:SMc02546
          Length = 538

 Score =  244 bits (623), Expect = 5e-69
 Identities = 172/531 (32%), Positives = 270/531 (50%), Gaps = 38/531 (7%)

Query: 3   DRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIA 62
           +R+ +FDTTLRDG+QTPG+  +VE+K+ IA  LD+FG+D +E G+P A+  + E  +   
Sbjct: 4   ERIYLFDTTLRDGQQTPGIDFSVEDKIAIASLLDQFGMDYVEGGYPGANPTDTEFFKCRR 63

Query: 63  GEELD------AEICGLARCVKGDIDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALE 116
            ++         +  G++      + A + A  D + +   + D H+   L  + EE L+
Sbjct: 64  TDKASFVAFGMTKRAGVSASNDPGLSALLSAKSDAICLVAKSWDYHVEVALGCTNEENLD 123

Query: 117 RAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMTP 173
                VE     G       E   D  + +  Y L   K   EAGA  V + DT G   P
Sbjct: 124 NIRASVEAVVASGREAMVDCEHFFDGYKANSAYALACAKTAFEAGARWVVLCDTNGGTQP 183

Query: 174 PEMYRLTAEVVDAVDVP---VSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGN 230
           PE+  + + V+ A  VP   + +H HND G AVANSLAAVEAG  Q+  T+NGIGER GN
Sbjct: 184 PEIREIVSAVI-AEGVPGANLGIHAHNDTGQAVANSLAAVEAGVRQIQGTLNGIGERCGN 242

Query: 231 ASLEQVV--MALKALYD--IELDVRTEMLVELSRLV---ERLTGVVVPPNTPIVGENAFA 283
           A+L  ++  +ALK  Y    E  +  E L EL++L    + L      P  P VG +AFA
Sbjct: 243 ANLVTLIATLALKETYSSRFETGIDAERLQELTKLAHAFDELLNRSPDPQAPYVGASAFA 302

Query: 284 HESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEE--QL 341
            ++GIH+  ++K   TYE + PE VG+ R++++    G+      L+  GI V+++  +L
Sbjct: 303 TKAGIHASALLKDPRTYEHVAPESVGNLRKVMVSDQGGKANFINALKRRGITVSKDDPRL 362

Query: 342 DEIVRRVKELGDKGKRVTEDD--LEAIARDVVGEVPESEAAVKLEEIAVMTGNKF----- 394
           D+++  VKE    G      D     +A  ++G VP+     ++E   VM   +F     
Sbjct: 363 DKLISIVKEREATGYAYEGADASFALLASRILGTVPD---FFRVESFRVMVERRFDANGK 419

Query: 395 ---TPTASVRVYLDGEEHEAASTGVGSVDAAIRALREAIEELG---MDVELKEYRLEAIT 448
                 A VRV +DGE   + + G G V+A   ALR+ + +      D+EL +Y++  + 
Sbjct: 420 LKTVSEAVVRVIVDGETMMSVAEGHGPVNALDLALRKDLGKYQSEIADLELADYKVRILN 479

Query: 449 GGTDALAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFVRGVNRLARRRRD 499
           GGT+A+  V +   D  G      G +++I+ AS +A +  +     + RD
Sbjct: 480 GGTEAVTRVLIESTDRSGARWWTVGVSDNIIDASFQALMDSIVYKLLKNRD 530


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: 517
Number of extensions: 16
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: 499
Length of database: 538
Length adjustment: 35
Effective length of query: 464
Effective length of database: 503
Effective search space:   233392
Effective search space used:   233392
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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