GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lysN in Sinorhizobium meliloti 1021

Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate SMc01578 SMc01578 aspartate aminotransferase

Query= SwissProt::P58350
         (410 letters)



>lcl|FitnessBrowser__Smeli:SMc01578 SMc01578 aspartate
           aminotransferase
          Length = 400

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

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

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

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

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

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

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

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


Lambda     K      H
   0.318    0.134    0.393 

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: 410
Length of database: 400
Length adjustment: 31
Effective length of query: 379
Effective length of database: 369
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 Sep 17 2021. The underlying query database was built on Sep 17 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 preprint on GapMind for carbon sources, or view the source code.

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