GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Echinicola vietnamensis KMM 6221, DSM 17526

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Echvi_0577 Echvi_0577 ornithine aminotransferase

Query= BRENDA::P42588
         (459 letters)



>lcl|FitnessBrowser__Cola:Echvi_0577 Echvi_0577 ornithine
           aminotransferase
          Length = 413

 Score =  209 bits (531), Expect = 2e-58
 Identities = 127/384 (33%), Positives = 203/384 (52%), Gaps = 35/384 (9%)

Query: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQ----ELLDPLRAMLAKTL 133
           D +G+++ D L  +   N GH +P ++  + +Q     L S+    ++L P    L +  
Sbjct: 40  DVEGEKYYDFLSSYSAVNQGHCHPRILQTLIDQAGTLTLTSRAFHNDVLGPFEKFLTEYF 99

Query: 134 A--ALTPGKLKYSFFCNSGTESVEAALKLAK--AYQS---PRGKFTFIATSGAFHGKSLG 186
               + P         N+G E VE A+K+A+   Y+    P  + T I     FHG++  
Sbjct: 100 GYDKVLP--------MNTGAEGVETAIKIARKWGYEKKGIPENEGTIIVAKNNFHGRTTT 151

Query: 187 ALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGV 246
            +S +   T RK F P  PGF  +P  +I+A++  L++ K    ++   ++EPIQGE GV
Sbjct: 152 VISFSNDETARKNFGPYTPGFVTIPHDDIDALKDVLSQSK----NIIGYLVEPIQGEAGV 207

Query: 247 ILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGV 306
            +P  GYL  V  +C + G L + DE+QTG+ RTGK+ AC+HE V+PD+L L KA+ GG 
Sbjct: 208 YVPKEGYLKEVAAVCKDHGVLFMADEIQTGIARTGKLLACDHEGVKPDMLILGKAISGGF 267

Query: 307 MPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDML 366
            P+ A +A + +  V+   P  H +TFGGNPL    A+  +NV+ ++ L   A++ G + 
Sbjct: 268 YPVSAVLADDHIMEVI--QPGQHGSTFGGNPLGAKVAMTALNVVKDEKLAENADKLGKLF 325

Query: 367 LDGFRQLAREYPDLVQEARGKGMLMAI---EFVDNEIGYNFASEMFRQRVLVAGTLNNAK 423
            +  +QL  +  DLV+  RGKG+L AI   +  D++  +     +    +L   T  N  
Sbjct: 326 RERIQQLV-DKSDLVELVRGKGLLNAIVINDTEDSDTAWRLCLALKENGLLAKPTHGN-- 382

Query: 424 TIRIEPPLTLTIEQ----CELVIK 443
            IR  PPL +T EQ    C+++ K
Sbjct: 383 IIRFAPPLVITEEQLHDCCDIIEK 406


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: 429
Number of extensions: 35
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: 413
Length adjustment: 32
Effective length of query: 427
Effective length of database: 381
Effective search space:   162687
Effective search space used:   162687
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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