GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Pseudomonas stutzeri RCH2

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate GFF657 Psest_0671 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::P23883
         (495 letters)



>lcl|FitnessBrowser__psRCH2:GFF657 Psest_0671 NAD-dependent aldehyde
           dehydrogenases
          Length = 506

 Score =  325 bits (833), Expect = 2e-93
 Identities = 191/484 (39%), Positives = 274/484 (56%), Gaps = 18/484 (3%)

Query: 23  FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82
           FINGE+      + F  + PV   P+A+  R  + DI++A+ AA    +   W  +S   
Sbjct: 22  FINGEFVEPVNGQYFTNLSPVNGQPIAEFPRSDAADIEKALDAAHAAADA--WGKTSVQA 79

Query: 83  RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142
           R  +L ++AD +E + E LA+ ET D GK +R +L  DIP AA   R++A  I    G  
Sbjct: 80  RSLILLQIADRIEQNLEMLAVTETWDNGKAVRETLNADIPLAADHFRYFAGCIRAQEGTS 139

Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202
           A    H  A    EP+GV+  I+PWNFP+L+  WKL PALAAGN V+LKP+E++PL    
Sbjct: 140 AEIDEHTAAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQTPLGITV 199

Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262
           L  +  +  LP GVLNVV G+G EAG+AL+    I  IAFTGST  G  ++K A ++ + 
Sbjct: 200 LMEVIGDL-LPPGVLNVVQGYGREAGEALASSKRIAKIAFTGSTPVGSHIMKRAAEAIIP 258

Query: 263 RVWLEAGGKSANIVFADCPD-----LQQAASATAAGIFYNQGQVCIAGTRLLLEESIADE 317
              +E GGKS NI F D        +++AA     G F+NQG+VC   +R L++ESI   
Sbjct: 259 ST-VELGGKSPNIYFEDIMQAEPTFIEKAAEGLVLG-FFNQGEVCTCPSRALVQESIYAP 316

Query: 318 FLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNA---- 373
           F+  + ++    + G PLD  T +G        D + S++   + +G  +L G  A    
Sbjct: 317 FMEAVMKKVAQIKRGDPLDTETMVGAQASQQQFDKIMSYLEIAKGEGAEVLTGGAAEKLE 376

Query: 374 -GLAAA--IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVW 430
             LA    I PT+    +    + +EEIFGPV+ VT F  E +AL +AND++YGLGA VW
Sbjct: 377 GSLATGYYIQPTLLKGTN-QMRVFQEEIFGPVIGVTTFKDEAEALAIANDTEYGLGAGVW 435

Query: 431 TRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIW 490
           TRD++RA+RM R +KAG V+ N Y+       FGGYK+SG GR+     L+ + + K + 
Sbjct: 436 TRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKRSGVGRETHKMILDSYQQTKNLL 495

Query: 491 ISLE 494
           IS +
Sbjct: 496 ISYD 499


Lambda     K      H
   0.317    0.133    0.389 

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: 526
Number of extensions: 20
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: 495
Length of database: 506
Length adjustment: 34
Effective length of query: 461
Effective length of database: 472
Effective search space:   217592
Effective search space used:   217592
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 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, 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