GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Klebsiella michiganensis M5al

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate BWI76_RS26375 BWI76_RS26375 aspartate aminotransferase family protein

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Koxy:BWI76_RS26375
          Length = 421

 Score =  199 bits (507), Expect = 1e-55
 Identities = 128/341 (37%), Positives = 189/341 (55%), Gaps = 23/341 (6%)

Query: 75  TLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAM--LAKT 132
           TL D +G E ID   G  + N GHR+P +++AV+ QL +   H+   + P  +   LA+ 
Sbjct: 33  TLWDIEGNEVIDFAAGIAVLNTGHRHPKIIAAVEQQL-QAFTHTAYQIVPYESYVTLAER 91

Query: 133 LAALTP--GKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSA 190
           + AL P  G  K +FF  +G E+VE A+K+A+AY    G  TF    G FHG++   ++ 
Sbjct: 92  INALAPIDGPAKTAFF-TTGAEAVENAVKIARAYTGRPGLITF---GGGFHGRTFMTMAL 147

Query: 191 TAK-STFRKPFMPLLPGFRHVPFGNIEAMRTALNECKK---------TGDDVAAVILEPI 240
           T K + ++  F P      H  + N     T  +  K            D VAA++LEPI
Sbjct: 148 TGKVAPYKIGFGPFPGSVYHAVYPNAAHGITTADAMKSLDRIFKADIAADQVAAIVLEPI 207

Query: 241 QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK 300
           QGEGG  + PP ++ A+R LCD  G L+I DEVQTG  RTGK+FA +H +V+PD++ +AK
Sbjct: 208 QGEGGFNVAPPEFMQALRALCDTHGILLIADEVQTGFARTGKLFAMQHYDVKPDLMTMAK 267

Query: 301 ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE 360
           +L GG  P+   +   EV       P     T+ GNPLA AAA A ++V+ E+ L  +AE
Sbjct: 268 SLAGG-FPLSGVVGRAEVMDA--PAPGGLGGTYAGNPLAVAAAHAVLDVIEEEQLCQRAE 324

Query: 361 QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIG 401
           + G  L +   Q AR+    + + RG+G ++A+EF D + G
Sbjct: 325 RLGSHLKEVLNQ-ARQSCPAIADVRGQGSMVAVEFNDPQTG 364


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: 427
Number of extensions: 21
Number of successful extensions: 6
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: 421
Length adjustment: 32
Effective length of query: 427
Effective length of database: 389
Effective search space:   166103
Effective search space used:   166103
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