GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Paraburkholderia bryophila 376MFSha3.1

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate H281DRAFT_02621 H281DRAFT_02621 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Burk376:H281DRAFT_02621
          Length = 447

 Score =  199 bits (507), Expect = 1e-55
 Identities = 129/413 (31%), Positives = 206/413 (49%), Gaps = 40/413 (9%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPL-HSQELLDPLRAMLAKTLA 134
           +VD+ G  +ID  GG  +  +GH +P V+ A+Q Q+ + P  H+          LA  L 
Sbjct: 24  IVDSTGTRYIDACGGAAVSCLGHSHPRVIEAIQRQVQQLPYAHTSFFTTEPAEALADLLI 83

Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSAT 191
              P  L + +F + G+E++EAALKLA+ Y   +G   +  FIA   ++HG +LGAL+  
Sbjct: 84  EAAPRNLGHVYFVSGGSEAMEAALKLARQYFVEKGQPERRHFIARRQSYHGNTLGALAIG 143

Query: 192 AKSTFRKPFMPLLPGFRHVP----FGNIEAMRTALNECKKTGDDVAAVILE--------- 238
             +  R+PF+P+L    HV     +   +A  T     ++  D++ A ILE         
Sbjct: 144 GNAWRREPFLPILIEAHHVTPCFAYREQQAGETDEAFAQRLADELEAKILELGAQSVAAF 203

Query: 239 ----PIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPD 294
                +    G + P   Y   +R +CD++G L+ILDEV +GMGRTG +FACE + V PD
Sbjct: 204 VAETVVGATAGAVPPVREYFRKIRAVCDKYGVLLILDEVMSGMGRTGHLFACEEDGVSPD 263

Query: 295 ILCLAKALGGGVMPIGATIATEEVFSVLFDNP--FLHTTTFGGNPLACAAALATINVLLE 352
           IL +AK LG G  PIGAT+ + E+F+ +      F H  T+ G+  ACAAAL    V+ E
Sbjct: 264 ILAIAKGLGAGYQPIGATLVSNEIFNTIVGGSGFFQHGHTYIGHATACAAALEVQKVIAE 323

Query: 353 QNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYN--------- 403
           + L    + +G+ L    R+    +P  + + RG+G+   +E V +              
Sbjct: 324 EQLLDNVKARGEQLRARLREWQANHP-FIGDVRGRGLFTGVELVQDRASKTAFDPKHKLH 382

Query: 404 --FASEMFRQRVLV---AGTLNN--AKTIRIEPPLTLTIEQCELVIKAARKAL 449
               SE  ++ ++V    GT++      + I PP   T  Q + +++    A+
Sbjct: 383 AIIKSEAMKRGLMVYPMGGTVDGRIGDHVLIAPPFITTSAQIDTIVERLADAI 435


Lambda     K      H
   0.320    0.135    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: 506
Number of extensions: 25
Number of successful extensions: 5
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: 459
Length of database: 447
Length adjustment: 33
Effective length of query: 426
Effective length of database: 414
Effective search space:   176364
Effective search space used:   176364
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: 51 (24.3 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