GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cola:Echvi_0577
          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 (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