GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Novosphingobium aromaticivorans DSM 12444

Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_011444108.1 SARO_RS02235 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::P96847
         (388 letters)



>NCBI__GCF_000013325.1:WP_011444108.1
          Length = 389

 Score =  149 bits (377), Expect = 1e-40
 Identities = 118/359 (32%), Positives = 169/359 (47%), Gaps = 15/359 (4%)

Query: 32  DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEP 91
           D+++LS G+P    P  V  A   AL      Y+  +G   LR A A  + R  G+ V P
Sbjct: 32  DVISLSVGEPDFATPAHVVQATKDALDAGDTKYTAVVGTAALRSAAALHFSRDLGLEVPP 91

Query: 92  DAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRFQ 151
             V+++ G       A LA  D GD V + SP +  Y  I+   G EVV++P      F+
Sbjct: 92  SQVIVSAGGKQAIFHALLATLDPGDEVLIPSPWWVSYPEIVRFAGAEVVDLPTDAAGGFR 151

Query: 152 PT-AQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASD-VRLISDEVYHGLV 209
            T AQ+ A I P  R +++ SP NPTG   P +EL A+         V ++SD++Y  L 
Sbjct: 152 ITAAQLEAAITPATRWLLLNSPGNPTGATYPAQELRALGEVLRRHPRVLVMSDDIYAPLR 211

Query: 210 YQGAPQTSCAWQ---TSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTIC 266
           Y      + A +    +   + V+  SK +AMTG+R+G    P  L  A+  L  + +  
Sbjct: 212 YGEGRHATLAVECPDLADRILTVSGVSKSHAMTGFRIGVAAGPAWLISAMGRLQSHSSGN 271

Query: 267 PPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRI-GIDRLAPTDGAFYVYAD 325
           P  +SQ AAV+AF        D     +   R ++   +  I G+    P DGAFY   D
Sbjct: 272 PASISQAAAVAAFEGPQDFLLDWR-ERFRARRDMVCARVNAIPGLSTPVP-DGAFYCMVD 329

Query: 326 VSDFTS---DSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEALRRI 381
            +   +   D  A C  LL ++GVA+ P   F    G    RISFA     +EEALRRI
Sbjct: 330 AAPLMARFGDDEALCLHLL-ESGVAVVPASAFG---GRDGFRISFAADEAKLEEALRRI 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: 424
Number of extensions: 21
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: 389
Length adjustment: 30
Effective length of query: 358
Effective length of database: 359
Effective search space:   128522
Effective search space used:   128522
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