GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Lutibaculum baratangense AMV1

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_023432784.1 N177_RS12830 betaine-aldehyde dehydrogenase

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



>NCBI__GCF_000496075.1:WP_023432784.1
          Length = 488

 Score =  352 bits (903), Expect = e-101
 Identities = 191/467 (40%), Positives = 280/467 (59%), Gaps = 7/467 (1%)

Query: 33  SGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKRKAKLIRFAD 92
           SG+    ++P +G  LA   +  + +  +A+E AR    S  W  ++ A+R   L R A 
Sbjct: 20  SGDALSSINPANGETLATGNAAAMPEIEQAIEAAREARRS--WMAMSAAERGRVLARVAA 77

Query: 93  LLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVAPTPHDQLGL 152
           +LR+  ++LA LE LD GKPI ++ + DI  AA    + A     V  E  P   D    
Sbjct: 78  ILRERRDDLARLEVLDTGKPIQEAPAADIDSAADCFEFFAGLTQIVQGEHIPFGDDGFAY 137

Query: 153 VTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIEAGI 212
             REP+G+   I  WN+P+ +A WK  PALA GN+++ KPSE +PLTA+ + ++  EAG 
Sbjct: 138 TRREPLGICAGIGAWNYPIQIASWKTAPALAAGNAMLFKPSEVTPLTALELGRIVEEAGA 197

Query: 213 PAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKRIWLEAGGKS 272
           P G+L++LPG G   G+ L+ H  +  +  TGS    K +M  A    +K + +E GGKS
Sbjct: 198 PPGLLSILPG-GRETGEILSTHPAIAKISVTGSVPTGKAVMASAA-GTLKHVTMELGGKS 255

Query: 273 PNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVVEALKGWKPG 332
             +VFADA DL  A  AA  A  + QGE+CT G+R+ VER + + FL       +  + G
Sbjct: 256 ALLVFADA-DLDDAVSAAMLANFYTQGEICTNGTRVFVERPVCEAFLEKAKARAEAIRIG 314

Query: 333 NPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE--TGGTYVEPTIFDG 390
           +PLDP+T +G L+  Q ++ V+ ++E G ++GA+L+ GGKR  +     G +++PTIF  
Sbjct: 315 DPLDPETQMGPLIHAQHLDKVMKFVENGVREGARLVTGGKRLTDGDFAKGNFMQPTIFAD 374

Query: 391 VTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHKTARAVRA 450
           V + M I  +EIFGPV+SV+ F++ EEA+  ANDTP+GLAAG+ T DIS+AH+ A  + A
Sbjct: 375 VLDQMTICMQEIFGPVMSVLPFESEEEALRRANDTPFGLAAGVMTRDISRAHRVAAKLEA 434

Query: 451 GSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497
           G VWVN Y+   +  PFGG K SG GR+  L AL+ YTE K+ ++ L
Sbjct: 435 GVVWVNHYNLTPIPMPFGGSKMSGLGRENGLAALDFYTERKSVYVNL 481


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: 622
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: 497
Length of database: 488
Length adjustment: 34
Effective length of query: 463
Effective length of database: 454
Effective search space:   210202
Effective search space used:   210202
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 24 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