GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ARO8 in Pseudomonas simiae WCS417

Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate GFF3717 PS417_19025 aspartate aminotransferase

Query= SwissProt::P58350
         (410 letters)



>FitnessBrowser__WCS417:GFF3717
          Length = 401

 Score =  374 bits (960), Expect = e-108
 Identities = 182/392 (46%), Positives = 257/392 (65%)

Query: 15  ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74
           + R+  I  S  +   A    ++ +G+ ++    GEPDFDTP H+  AAS A+H G+T Y
Sbjct: 6   SDRVLGIAPSPSIAANALVTELRAQGRDIVNFTVGEPDFDTPAHILAAASQAMHNGDTHY 65

Query: 75  TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134
           T+  GT  L++AI  K Q++N LAY LDE+    G K ++++A+ A+L+ GDEVI+ TPY
Sbjct: 66  TSTTGTLALRQAICLKLQQDNDLAYGLDEVVAGCGGKHVIYHALAATLNRGDEVIVHTPY 125

Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194
           W SY DI  + +  PV+I  D S GF+L+ + LE AIT RT+WV+LNSP+NPSGA Y+  
Sbjct: 126 WVSYPDIARLNDATPVIIPGDESLGFKLSPDALEQAITARTKWVILNSPNNPSGAVYNET 185

Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254
           +   L +VL RHPHV ++ D++YEH +Y   R V   +L P LK RTL VNG SK YAMT
Sbjct: 186 ELLALAQVLRRHPHVLIMADEIYEHFIYGRARHVPLTRLAPDLKPRTLIVNGASKGYAMT 245

Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314
           GWR+G+  GP  LI A+A + SQ T+CPSS+SQAA+VAA  G Q  +    E +Q+RR  
Sbjct: 246 GWRLGFGAGPAWLIAAIAKLLSQTTTCPSSLSQAAAVAAFTGDQAPIAAMREEYQQRRAR 305

Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374
           ++  L  I GL C  P+GAFY F+  +G++GK+TP G R+ +DT    YLL D  +A V 
Sbjct: 306 MLALLADIPGLSCTPPDGAFYVFANVSGLMGKLTPQGDRLDSDTQLVDYLLRDYGLATVS 365

Query: 375 GSAFGLSPFFRISYATSEAELKEALERIAAAC 406
           G+A+G+SP+ R+S+A+S   ++E   R+  AC
Sbjct: 366 GAAYGMSPYVRLSFASSSEVIEEGCRRLKDAC 397


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: 468
Number of extensions: 18
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: 401
Length adjustment: 31
Effective length of query: 379
Effective length of database: 370
Effective search space:   140230
Effective search space used:   140230
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:

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