GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Sinorhizobium meliloti 1021

Align aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate SMc04386 SMc04386 aspartate aminotransferase B protein

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__Smeli:SMc04386
          Length = 410

 Score =  470 bits (1210), Expect = e-137
 Identities = 231/392 (58%), Positives = 286/392 (72%)

Query: 5   ADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKY 64
           A  +S +  S  + +  +A  +K +G+ VI LGAGEPDFDTP+++K+AA DAI RGETKY
Sbjct: 15  ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74

Query: 65  TPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPY 124
           T + G PEL++AI +KF+REN L Y   +  V TG KQILFNA MA+L+PGDEV+IP PY
Sbjct: 75  TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134

Query: 125 WVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHE 184
           W SY ++V +C G PV +     + F+L AE L+ AITP+T+W + NSPSNPSGAAYS  
Sbjct: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194

Query: 185 ELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMT 244
           + + L +VL++HPHVW+L DDMYEH+ Y  FRF TP ++EPGL  RTLT+NGVSKAYAMT
Sbjct: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254

Query: 245 GWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDL 304
           GWRIGYA GP  LIKAM ++Q Q TS  +SI+Q A+V ALNGPQDF+    E FQ RRDL
Sbjct: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314

Query: 305 VVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVH 364
           VV+ LN   G+ C  PEGAFY +  CAG++GK  PSGK I+TD DF + LLE   VAVV 
Sbjct: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374

Query: 365 GSAFGLGPNFRISYATSEALLEEACRRIQRFC 396
           GSAFGL P FRISYATSEA L+EA  RI   C
Sbjct: 375 GSAFGLSPFFRISYATSEAELKEALERIAAAC 406


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: 503
Number of extensions: 15
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: 410
Length adjustment: 31
Effective length of query: 369
Effective length of database: 379
Effective search space:   139851
Effective search space used:   139851
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 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