GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ARO8 in Pseudomonas putida KT2440

Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate PP_1872 PP_1872 glutamate-pyruvate aminotransferase

Query= curated2:P63499
         (429 letters)



>lcl|FitnessBrowser__Putida:PP_1872 PP_1872 glutamate-pyruvate
           aminotransferase
          Length = 403

 Score =  570 bits (1469), Expect = e-167
 Identities = 278/402 (69%), Positives = 334/402 (83%), Gaps = 1/402 (0%)

Query: 28  FAQSAKLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQALP 87
           F++S KL +V Y+IRGPV +HA RLE EGHRILKLNIGNPAPFGFEAPD I++D+I+ LP
Sbjct: 3   FSKSNKLANVCYDIRGPVLKHAKRLEEEGHRILKLNIGNPAPFGFEAPDEILQDVIRNLP 62

Query: 88  YAQGYSDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITMTLQALLDNGDQV 147
            AQGYSDS+G+ SAR+AV+ +Y          ++D+YLGNGVSELI M++QALL+NGD+V
Sbjct: 63  TAQGYSDSKGLFSARKAVM-QYCQQKDIEGVTIEDIYLGNGVSELIVMSMQALLNNGDEV 121

Query: 148 LIPSPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPTG 207
           LIP+PDYPLWTA+ SLAGG PVHYLCDE   W PD+ D+++KIT  TKALV+INPNNPTG
Sbjct: 122 LIPAPDYPLWTAAVSLAGGKPVHYLCDEQADWFPDLEDIKAKITPNTKALVIINPNNPTG 181

Query: 208 AVYSCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIAPDMLCLTFNGLSKAY 267
           AVYS E+L  M++LAR+H L++ +DEIYDKILYD+A HIS AS+APD+LCLTFNGLSK+Y
Sbjct: 182 AVYSKELLLGMLELARQHNLVVFSDEIYDKILYDEAVHISTASLAPDLLCLTFNGLSKSY 241

Query: 268 RVAGYRAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLVLP 327
           RVAG+R+GWL I+GPK HA S+IEGI +LANMRLC NVPAQHAIQ ALGG+QSI DLVLP
Sbjct: 242 RVAGFRSGWLIISGPKHHAHSYIEGIDMLANMRLCANVPAQHAIQTALGGYQSINDLVLP 301

Query: 328 GGRLLEQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEKIL 387
            GRLLEQR+  +  LN+IPGVSCVKP GALYAFPR+DP+V  I +DE+  LDLLLSEK+L
Sbjct: 302 PGRLLEQRNRTYELLNDIPGVSCVKPMGALYAFPRIDPKVCPILNDEKFALDLLLSEKLL 361

Query: 388 VTQGTGFNWPAPDHLRLVTLPWSRDLAAAIERLGNFLVSYRQ 429
           + QGT FNWP PDH R+VTLP   DL AAI R+GNFL  Y Q
Sbjct: 362 IVQGTAFNWPWPDHFRVVTLPRVDDLEAAIGRIGNFLKGYSQ 403


Lambda     K      H
   0.320    0.138    0.419 

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: 621
Number of extensions: 16
Number of successful extensions: 2
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: 429
Length of database: 403
Length adjustment: 31
Effective length of query: 398
Effective length of database: 372
Effective search space:   148056
Effective search space used:   148056
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 (21.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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