GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Klebsiella michiganensis M5al

Align Putrescine aminotransferase; PAT; PATase; EC 2.6.1.82; Cadaverine transaminase; EC 2.6.1.-; Putrescine transaminase; Putrescine--2-oxoglutaric acid transaminase (uncharacterized)
to candidate BWI76_RS26375 BWI76_RS26375 aspartate aminotransferase family protein

Query= curated2:B7LZM2
         (459 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS26375 BWI76_RS26375 aspartate
           aminotransferase family protein
          Length = 421

 Score =  200 bits (508), Expect = 8e-56
 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 VAALTP--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    0.136    0.395 

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: 440
Number of extensions: 22
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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