GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvE in Sphingomonas koreensis DSMZ 15582

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Ga0059261_2226 Ga0059261_2226 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::Q02635
         (400 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_2226 Ga0059261_2226
           Aspartate/tyrosine/aromatic aminotransferase
          Length = 399

 Score =  482 bits (1240), Expect = e-141
 Identities = 244/394 (61%), Positives = 286/394 (72%)

Query: 7   ALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTP 66
           AL+R++PSAT+A++ +  ELK +G DVIGLGAGEPDFDTPD +K+AAI+AI +G TKYT 
Sbjct: 6   ALNRIQPSATLAMTSRVFELKRQGIDVIGLGAGEPDFDTPDFVKEAAIEAIRKGITKYTN 65

Query: 67  VSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWV 126
           V G PEL+ AI  KF R+N L Y   Q  V +GGK  LFNAF AT++ GDEVVIPAPYWV
Sbjct: 66  VDGTPELKAAIVGKFARDNGLTYAENQISVNSGGKHTLFNAFCATIDAGDEVVIPAPYWV 125

Query: 127 SYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEEL 186
           SYP++V   GG PVF+    E N+K+K E L+ AIT +TKW V NSPSNP+GAAYS  EL
Sbjct: 126 SYPDVVEFAGGKPVFIAAGAEANYKIKPEQLEAAITARTKWVVLNSPSNPTGAAYSAAEL 185

Query: 187 KALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGW 246
           KAL +VL +HP+V +  DDMYEH+ Y  F FAT  +V P LYERTLT NGVSKAYAMTGW
Sbjct: 186 KALGEVLERHPNVLIYADDMYEHILYDGFEFATIAQVCPSLYERTLTANGVSKAYAMTGW 245

Query: 247 RIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVV 306
           RIGYA GP  LIKAM  +Q Q TS   S++Q A+V ALNG Q F+      FQ RRDLVV
Sbjct: 246 RIGYAGGPQWLIKAMGKLQSQSTSNPCSVSQAASVAALNGDQSFLKDRAAAFQKRRDLVV 305

Query: 307 SMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVHGS 366
           SML Q  G++CP PEGAFYVYP  + LIGKT P G VI+TDE  V  LL+   VA VHG 
Sbjct: 306 SMLGQINGMNCPRPEGAFYVYPEFSQLIGKTTPKGLVIDTDETMVGYLLDDAKVAAVHGG 365

Query: 367 AFGLGPNFRISYATSEALLEEACRRIQRFCAACR 400
           AFG  P  RISYATSE +L EAC RIQ  CAA R
Sbjct: 366 AFGFSPALRISYATSEDVLAEACGRIQEACAALR 399


Lambda     K      H
   0.318    0.134    0.402 

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: 518
Number of extensions: 14
Number of successful extensions: 1
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: 400
Length of database: 399
Length adjustment: 31
Effective length of query: 369
Effective length of database: 368
Effective search space:   135792
Effective search space used:   135792
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 (21.7 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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