GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Klebsiella michiganensis M5al

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate BWI76_RS07615 BWI76_RS07615 betaine-aldehyde dehydrogenase

Query= BRENDA::Q88RC0
         (480 letters)



>FitnessBrowser__Koxy:BWI76_RS07615
          Length = 490

 Score =  313 bits (801), Expect = 1e-89
 Identities = 174/483 (36%), Positives = 274/483 (56%), Gaps = 9/483 (1%)

Query: 6   AQLFRQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWR 65
           +++  QQ YI+G ++ A +G+T +  NPA GEV+ TV   G  +  RA+++A K    W 
Sbjct: 2   SRMAEQQLYIDGGYVSATSGKTFETINPANGEVLATVQAAGREDVDRAVKSAQKGQKIWA 61

Query: 66  ALTAKERSAKLRRWFELMIENQDDLARLMTTEQGKPLAE-AKGEIAYAASFIEWFAEEAK 124
           A++A ERS  LR+  +++    D+LARL T + GKPL+E A  +I   A  +E++A    
Sbjct: 62  AMSAMERSRILRKAVDILRARNDELARLETLDTGKPLSETAAVDIVTGADVLEYYAGLIP 121

Query: 125 RIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQ 184
            + G  IP  +    +   ++P+GV A I  WN+P  +   K+ PALAAG  M+ KP+  
Sbjct: 122 ALEGSQIP-LRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEV 180

Query: 185 TPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLM-E 243
           TP +AL L E+   AG+PAGV +V+ G+  E G  LT +  + K+SFTG    G+++M  
Sbjct: 181 TPLTALKLAEIYREAGLPAGVFNVLPGTGAETGQYLTEHPDIAKISFTGGVASGKKVMAN 240

Query: 244 ECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYD 303
             A  +K+V++ELGG +P IV +DA LD A + A+++ + ++GQ C    R++V   +  
Sbjct: 241 AAASSLKEVTMELGGKSPLIVCEDASLDLAADIAMMANFYSSGQVCTNGTRVFVPTRLKA 300

Query: 304 AFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIEG 363
           AF EK+ A VA+++ G+   E T  GPL+       V  +IE    +GA++L GG+ ++G
Sbjct: 301 AFEEKILARVARIRPGDLFAESTNFGPLVSFPHRDNVLRYIETGKQEGARLLCGGEALKG 360

Query: 364 NFFE------PTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFY 417
             F+      PT+  D      + +EE FGP+  +  + DE E +  +N TE+GLA+   
Sbjct: 361 EGFDRGAWVAPTVFTDCDDQMTIVREEIFGPVMSILSYDDEEEALRRANATEYGLAAGVV 420

Query: 418 ARDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLC 477
             D++R  R+   LE G+  INT   S    P GG K SG+GRE     +  Y +IK + 
Sbjct: 421 TPDLNRAHRLIHRLEAGICWINTWGESPAEMPVGGYKHSGIGRENGVQTLHSYTQIKSIQ 480

Query: 478 ISV 480
           + +
Sbjct: 481 VEM 483


Lambda     K      H
   0.317    0.134    0.384 

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: 565
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: 480
Length of database: 490
Length adjustment: 34
Effective length of query: 446
Effective length of database: 456
Effective search space:   203376
Effective search space used:   203376
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