GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Pseudomonas simiae WCS417

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF3406 PS417_17430 aldehyde dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__WCS417:GFF3406
          Length = 506

 Score =  320 bits (819), Expect = 9e-92
 Identities = 182/481 (37%), Positives = 280/481 (58%), Gaps = 18/481 (3%)

Query: 7   INGELVSG-EGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAE 65
           I GE V+   GE     +P TG+V+ E   ++A  +D A+ AA AA   WG+T+P+ R+ 
Sbjct: 23  IGGEFVAPLSGEYFTNTSPVTGEVIAEFPRSNAADIDKALDAAHAAADAWGKTSPQDRSL 82

Query: 66  CLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGE 125
            LLK+AD IE++ +V A  ES + GK +    N ++P   D FR+FAG  R   G AA  
Sbjct: 83  VLLKIADRIEQHLEVLAVTESWDNGKAVRETLNADVPLAADHFRYFAGCIRAQEGGAAE- 141

Query: 126 YLEGHTSMIR-RDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKL 184
            +  HT+     +PLGVV  I PWN+PL+MAAWKLAPALAAGNC+VLKP+E TPL+ +  
Sbjct: 142 -INEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVLKPAEQTPLSIMVF 200

Query: 185 AELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTH 244
           AEL  D+ P GV+NI+ G G+  G+ L    ++  ++ TGS   G HI+   A ++  + 
Sbjct: 201 AELINDLLPPGVLNIVQGFGREAGEALATSKRIAKIAFTGSTPIGAHIMHAAAENLIPST 260

Query: 245 MELGGKAPVIVFDD------ADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVE 298
           +ELGGK+P I F+D        IE   EG+    ++N G+ CT   R   Q+ IYD  ++
Sbjct: 261 VELGGKSPNIFFEDIMQAEPQFIEKAAEGL-VLAFFNQGEVCTCPSRALVQESIYDDFMK 319

Query: 299 KLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGG--EKRKG- 355
            +   +  +K G P D  T +G  +S    +++   ++ A+  G  +++TGG  E+ +G 
Sbjct: 320 VVMKKIVKIKRGNPLDTETMVGAQASEQQYDKILSYLKIAQEEG-AELLTGGAAERLEGD 378

Query: 356 --NGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTK 413
             +GYY  PTLL G      + Q+E+FGPVV +T F +E + +  ANDS++GL + +WT+
Sbjct: 379 LSSGYYIQPTLLKGH-NKMRVFQEEIFGPVVGITTFKDEAEALAIANDSEFGLGAGLWTR 437

Query: 414 DVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473
           D+ RA+R+   ++ G  W N + +  +    GG K SG G++     L+ Y   ++++V 
Sbjct: 438 DINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRENHKMMLDHYQQTKNLLVS 497

Query: 474 H 474
           +
Sbjct: 498 Y 498


Lambda     K      H
   0.317    0.134    0.397 

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: 610
Number of extensions: 30
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: 474
Length of database: 506
Length adjustment: 34
Effective length of query: 440
Effective length of database: 472
Effective search space:   207680
Effective search space used:   207680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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