GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Escherichia coli BW25113

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 15866 b1748 succinylornithine transaminase, PLP-dependent (NCBI)

Query= curated2:B7LZM2
         (459 letters)



>FitnessBrowser__Keio:15866
          Length = 406

 Score =  193 bits (491), Expect = 8e-54
 Identities = 127/369 (34%), Positives = 191/369 (51%), Gaps = 23/369 (6%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAK-QPLHSQELLDPLRAMLAKTVA 134
           L D QG+E+ID  GG  +  +GH +P +  A+  Q +K     +    +P+  +  K + 
Sbjct: 33  LWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEPVLRLAKKLID 92

Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPR---GKFTFIATSGAFHGKSLGALSAT 191
           A    ++   FFCNSG E+ EAALKLA+ +   R    K   +A   AFHG++L  +SA 
Sbjct: 93  ATFADRV---FFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHGRTLFTVSAG 149

Query: 192 AKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPP 251
            +  + + F PL    RH  + +I +    ++      D   AVI+EPIQGEGGV+    
Sbjct: 150 GQPAYSQDFAPLPADIRHAAYNDINSASALID------DSTCAVIVEPIQGEGGVVPASN 203

Query: 252 GYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGA 311
            +L  +R+LC+   AL+I DEVQTG+GRTG+++A  H  V PD+L  AKALGGG  P+GA
Sbjct: 204 AFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTAKALGGG-FPVGA 262

Query: 312 TIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371
            +ATEE   V+      H TT+GGNPLA A A   + ++    +    +Q+ D  ++   
Sbjct: 263 LLATEECARVM--TVGTHGTTYGGNPLASAVAGKVLELINTPEMLNGVKQRHDWFVERLN 320

Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGT---LNNAKTIRIE 428
            +   Y  L  E RG G+L+          Y   ++   Q    AG    +     +R  
Sbjct: 321 TINHRY-GLFSEVRGLGLLIGCVL---NADYAGQAKQISQEAAKAGVMVLIAGGNVVRFA 376

Query: 429 PPLTLTIEQ 437
           P L ++ E+
Sbjct: 377 PALNVSEEE 385


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: 441
Number of extensions: 28
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: 406
Length adjustment: 32
Effective length of query: 427
Effective length of database: 374
Effective search space:   159698
Effective search space used:   159698
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