GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Sinorhizobium meliloti 1021

Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate SMc01340 SMc01340 aminotransferase

Query= SwissProt::P96847
         (388 letters)



>FitnessBrowser__Smeli:SMc01340
          Length = 385

 Score =  349 bits (896), Expect = e-101
 Identities = 187/386 (48%), Positives = 249/386 (64%), Gaps = 8/386 (2%)

Query: 4   RVALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLG 63
           +++ R+ V PF+ MDV   A  R+ +   +++++ GQP+  AP+    AA  AL   +LG
Sbjct: 3   QMSKRSAVEPFHAMDVLAEATRRRDSGHPVISMAVGQPAHPAPKAALDAARRALDHGRLG 62

Query: 64  YSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASP 123
           Y+ ALG   L+ AIAA Y  RHGIT++P  + +TTGSS GF LAFLA FD GDRVA+A P
Sbjct: 63  YTDALGTHSLKRAIAAHYHSRHGITLDPQRIAVTTGSSAGFNLAFLALFDPGDRVAIARP 122

Query: 124 GYPCYRNILSALGCEVVEIPCGPQTRFQPTAQML----AEIDPPLRGVVVASPANPTGTV 179
           GYP YRNI++ALG EVVEI    +  F  T   L    A    PL+GV++ASPANPTGTV
Sbjct: 123 GYPAYRNIMAALGLEVVEIEANAEAGFTLTPDSLEGAAARAGKPLKGVLLASPANPTGTV 182

Query: 180 IPPEELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMT 239
               +L A+A +C    +  ISDE+YHGL + G   T  A + + +AVV+NSFSKYY MT
Sbjct: 183 TGKAQLKALADYCRDHSIAFISDEIYHGLTFAGEETT--ALEVADDAVVINSFSKYYCMT 240

Query: 240 GWRLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRS 299
           GWR+GW+++P    RA + +  +  I PP LSQIAA +A    A  E DG   +YA NR+
Sbjct: 241 GWRIGWMVLPEARVRAFERIAQSLYISPPELSQIAAEAAL--GAHEELDGYKRAYAANRA 298

Query: 300 LLLDGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARG 359
           LLL+ L +IG    +P DGAFY YADVS FT+DS+AF  ++LA+  VA  PG DFD   G
Sbjct: 299 LLLERLPQIGFSIASPMDGAFYAYADVSRFTNDSMAFARRMLAEIDVAATPGFDFDPLEG 358

Query: 360 GSFVRISFAGPSGDIEEALRRIGSWL 385
              +R S+AG + ++EEA+ RI  WL
Sbjct: 359 HRTMRFSYAGAATEMEEAMNRIARWL 384


Lambda     K      H
   0.321    0.136    0.416 

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: 468
Number of extensions: 24
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: 388
Length of database: 385
Length adjustment: 30
Effective length of query: 358
Effective length of database: 355
Effective search space:   127090
Effective search space used:   127090
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 (21.9 bits)
S2: 50 (23.9 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