GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Pseudomonas simiae WCS417

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF5142 PS417_26340 betaine-aldehyde dehydrogenase

Query= metacyc::MONOMER-11560
         (497 letters)



>FitnessBrowser__WCS417:GFF5142
          Length = 490

 Score =  367 bits (942), Expect = e-106
 Identities = 192/479 (40%), Positives = 282/479 (58%), Gaps = 5/479 (1%)

Query: 21  RAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAP 80
           + +I+G YTDA S  TFE ++P +G  LA+V      D  RAV +A       +W+ +  
Sbjct: 8   KLYIDGGYTDAGSDATFEAINPANGEVLAQVQRATKEDVERAVVSAEK--GQKIWAAMTA 65

Query: 81  AKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYD 140
            +R   L R  D+LR+  +ELA LETLD GK   ++  +DI   A  + + A  +  +  
Sbjct: 66  MERSRILRRAVDILRERNDELAALETLDTGKAFSETKYVDIVTGADVLEYYAGLVPAIEG 125

Query: 141 EVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTA 200
           E  P          REP+GVV  I  WN+P+ +A WK  PALA GN+++ KPSE + LT 
Sbjct: 126 EQIPLRDTSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTT 185

Query: 201 IRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESN 260
           +++A++  EAG+PAGV NVL G G  VG  L  H  ++ + FTG T   K++M  A  S+
Sbjct: 186 LKLAEIYTEAGVPAGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTDTGKKVMASASSSS 245

Query: 261 MKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLP 320
           +K + +E GGKSP IVF DA DL  AA+ A  A  ++ G+VCT G+R+ V + ++  F  
Sbjct: 246 LKEVTMELGGKSPLIVFEDA-DLDRAADIAMMANFYSSGQVCTNGTRVFVPKHLQAAFEA 304

Query: 321 MVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL--EET 378
            +VE +   + GNP D  T  G LV    M +VL YI  G ++GA++L GG R    E  
Sbjct: 305 KIVERVARIRVGNPQDDNTNFGPLVSFAHMESVLGYIAKGKEEGARVLCGGDRLTDGEFA 364

Query: 379 GGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDI 438
            G +V PT+F   T+ M I +EEIFGPV+S++ ++T EE +  ANDT +GLAAG+ T D+
Sbjct: 365 KGAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTDFGLAAGLVTKDL 424

Query: 439 SKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497
           ++AH+    + AG  W+N +   D   P GG+KQSG GR+  + +L  +T +K+  ++L
Sbjct: 425 NRAHRVIHQLEAGICWINAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVEL 483


Lambda     K      H
   0.316    0.132    0.390 

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: 633
Number of extensions: 27
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: 497
Length of database: 490
Length adjustment: 34
Effective length of query: 463
Effective length of database: 456
Effective search space:   211128
Effective search space used:   211128
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 (21.6 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