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_023433101.1 N177_RS14415 aldehyde dehydrogenase

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



>NCBI__GCF_000496075.1:WP_023433101.1
          Length = 492

 Score =  335 bits (860), Expect = 2e-96
 Identities = 196/480 (40%), Positives = 276/480 (57%), Gaps = 9/480 (1%)

Query: 21  RAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAP 80
           R +I+G + +  +G +FE + P  G   A + + + AD +RAV  A   F+   WS+L  
Sbjct: 7   RNYIDGAFCEGGAG-SFESVDPATGEAWANMPAANAADVDRAVRAADRAFHDPSWSRLTA 65

Query: 81  AKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYD 140
            +R   L R ADL+ +N + LA LET D GK I ++S+  I   A    + A   DK+  
Sbjct: 66  TQRGKLLYRLADLVAENAQALAELETRDTGKIIRETSA-QIAYVADYYRYYAGLADKI-- 122

Query: 141 EVAPTPHDQLGLVT---REPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSP 197
           E A  P D+  + T   REP+GVV A+VPWN  L ++  KLGPALA G +VVLK SE  P
Sbjct: 123 EGAHLPIDKPDMETYLRREPIGVVAAVVPWNSQLFLSAVKLGPALAAGCTVVLKASEDGP 182

Query: 198 LTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAG 257
              +  A+L  +AG P GV+N+L G+G   G ALA H  V  + FTG    A+ ++ ++ 
Sbjct: 183 APLLAFARLVDQAGFPPGVVNILTGFGDQCGSALASHPLVARIAFTGGPATARHIVRHSA 242

Query: 258 ESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317
           E N+  + LE GGKSP +VF DA DL + A A  + I    G+ C AGSRL+V+R IKD 
Sbjct: 243 E-NLAAVTLELGGKSPVVVFEDA-DLDSVANAVVAGIFAATGQSCVAGSRLIVQRGIKDA 300

Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE 377
            L  +V+  +  + G+P   +T +G L   +Q+  +   I      G +L+ GG R    
Sbjct: 301 LLERLVQKARAIRIGDPQAQETEMGPLATARQLRHIEDVIARSLAAGGRLVTGGGRPDGF 360

Query: 378 TGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSD 437
             G Y EPTI D     +   +EE+FGPVLSV+ F+   EAV  AN TPYGLA+G++T+ 
Sbjct: 361 PAGHYFEPTIIDCDATTIPSVEEELFGPVLSVLGFEEETEAVEFANRTPYGLASGVFTAS 420

Query: 438 ISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497
           +++AH+  RA+RAG VWVN Y       PFGG+  SG+GR+  L A   YT  KA WI++
Sbjct: 421 LTRAHRMIRAIRAGVVWVNTYRAVSPIMPFGGYGLSGSGREGGLDAALDYTRTKAVWIRV 480


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: 634
Number of extensions: 25
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: 492
Length adjustment: 34
Effective length of query: 463
Effective length of database: 458
Effective search space:   212054
Effective search space used:   212054
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