GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Pedobacter sp. GW460-11-11-14-LB5

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate CA265_RS18530 CA265_RS18530 aspartate aminotransferase family protein

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Pedo557:CA265_RS18530
          Length = 382

 Score =  186 bits (472), Expect = 1e-51
 Identities = 125/372 (33%), Positives = 193/372 (51%), Gaps = 20/372 (5%)

Query: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137
           D   Q+++D  GG  + ++GH NP  V+ + +QL K   +S  +  PL+  LA+ L  ++
Sbjct: 24  DANDQQYLDLYGGHAVISIGHTNPHYVNRLTDQLNKVGFYSNSVKIPLQVQLAEKLGEVS 83

Query: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFR 197
             K    F CNSG E+ E ALKLA  Y    G+   IA +GAFHG++  A++ T      
Sbjct: 84  GKKDFQLFLCNSGAEANENALKLASFYN---GRKKVIAFTGAFHGRTSLAVAVTDNPKIV 140

Query: 198 KPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAV 257
            P +        +PF N  A+       K  G++++AVI+E IQG GG+      +L  +
Sbjct: 141 AP-VNQTENVIFLPFNNEIALEETF---KAQGNEISAVIIEGIQGVGGIKEASKSFLQKI 196

Query: 258 RKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEE 317
           R LCDE+ A+ I D VQ G GRTG  ++ ++  V+ D+  +AK +G G    G +IA++ 
Sbjct: 197 RSLCDEYNAVYIADSVQCGYGRTGSFYSHDYSGVEADVYTMAKGMGNGFPVAGISIASK- 255

Query: 318 VFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREY 377
            F           TTFGGN LACAAALA + V+ + NL   AE+ G+ L+   ++     
Sbjct: 256 -FKPWHGE---LGTTFGGNHLACAAALAVLEVMEKDNLIKNAEEVGNYLIAELKKF---- 307

Query: 378 PDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTIEQ 437
            + V E RG+G+++ IE +  E+ +     +F   +       N   IR+ P L LT   
Sbjct: 308 -EQVVEVRGRGLMIGIE-LPAELAHVKKELLFTHHIFTGEAKPN--VIRLLPALNLTKAH 363

Query: 438 CELVIKAARKAL 449
            +  + A  KA+
Sbjct: 364 ADEFLAAFEKAV 375


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: 316
Number of extensions: 10
Number of successful extensions: 4
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: 382
Length adjustment: 32
Effective length of query: 427
Effective length of database: 350
Effective search space:   149450
Effective search space used:   149450
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: 50 (23.9 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