GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ARO8 in Dechlorosoma suillum PS

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate Dsui_2909 Dsui_2909 aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::Q8YTF2
         (403 letters)



>FitnessBrowser__PS:Dsui_2909
          Length = 395

 Score =  355 bits (910), Expect = e-102
 Identities = 177/380 (46%), Positives = 246/380 (64%), Gaps = 3/380 (0%)

Query: 11  RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70
           RI++LPPYVF    ELK  AR +G D+ID+ MGNPDGATP+ +VD  + A Q    HGY 
Sbjct: 6   RIKRLPPYVFNITGELKMAARRRGEDIIDMSMGNPDGATPKHIVDKMVDATQRGDTHGYS 65

Query: 71  PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130
             +G    R+AI +WY RRY V  DPDSEA+  +GSKEGL+HL +A ++ GD VLVP+P+
Sbjct: 66  VSKGIPRLRKAICDWYLRRYNVEFDPDSEAVVTIGSKEGLAHLMLATLDRGDTVLVPNPS 125

Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190
           YP H  G +IAG    S+ +  + D+  +L     E   K K++   +PSNPT      +
Sbjct: 126 YPIHIYGAIIAGANTRSVRMTDDVDFFEELQRAIRECTPKPKMMILGFPSNPTARCVELD 185

Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250
           FFE +VA A++++IL+VHDL YA++ FDGY+  S++E+PGA+D+ VEF T+SK+YNMAGW
Sbjct: 186 FFERVVALAKEHDILVVHDLAYADIVFDGYRAPSIMEVPGARDVAVEFFTMSKSYNMAGW 245

Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310
           RVG++VGN+ +   L  +K+  DYG F  +Q A+  AL  P   + EV+Q Y  RR+ L 
Sbjct: 246 RVGYMVGNKELCAALARIKSYHDYGTFTPIQVASVIALDGPQDCVEEVRQTYELRRNVLA 305

Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367
           +GL E GW V   KA+MY+W K P     +GS +FA  LL +  V V+PG  FG  G+ +
Sbjct: 306 KGLHEAGWMVEVPKASMYIWAKIPEPYAHLGSLEFAKKLLAEAKVAVSPGIGFGDYGDDH 365

Query: 368 VRISLIADCDRLGEALDRIK 387
           VR +LI +  R  +A+  IK
Sbjct: 366 VRFALIENEARTRQAIRGIK 385


Lambda     K      H
   0.321    0.140    0.427 

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: 469
Number of extensions: 19
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: 403
Length of database: 395
Length adjustment: 31
Effective length of query: 372
Effective length of database: 364
Effective search space:   135408
Effective search space used:   135408
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 (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