GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Klebsiella michiganensis M5al

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate BWI76_RS07615 BWI76_RS07615 betaine-aldehyde dehydrogenase

Query= SwissProt::P42236
         (488 letters)



>FitnessBrowser__Koxy:BWI76_RS07615
          Length = 490

 Score =  325 bits (833), Expect = 2e-93
 Identities = 190/489 (38%), Positives = 275/489 (56%), Gaps = 9/489 (1%)

Query: 1   MSVITEQNTYLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEA 60
           MS + EQ  Y   I+G +V + SG   +  NPA+  +++  VQ +  EDV+RAV +A + 
Sbjct: 1   MSRMAEQQLY---IDGGYVSATSGKTFETINPAN-GEVLATVQAAGREDVDRAVKSAQKG 56

Query: 61  KTAWRKLTGAERGQYLYKTADIMEQRLEEIAACATREMGKTLPE-AKGETARGIAILRYY 119
           +  W  ++  ER + L K  DI+  R +E+A   T + GK L E A  +   G  +L YY
Sbjct: 57  QKIWAAMSAMERSRILRKAVDILRARNDELARLETLDTGKPLSETAAVDIVTGADVLEYY 116

Query: 120 AGEGMRKTGDVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVI 179
           AG      G  IP  D  + ++T R PLGVV  I  WN+P+ I +WK APAL  GN ++ 
Sbjct: 117 AGLIPALEGSQIPLRDS-SFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIF 175

Query: 180 KPATETAVTCAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGK 239
           KP+  T +T  K+   + EAGLPAGV N++ G G+  GQ L EH  +  ++FTG    GK
Sbjct: 176 KPSEVTPLTALKLAEIYREAGLPAGVFNVLPGTGAETGQYLTEHPDIAKISFTGGVASGK 235

Query: 240 -IIGQAALARGAKYQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQ 298
            ++  AA +   +  +E+GGK+P+IV +DA L+ AA+  +   F S+GQ CT  +RV V 
Sbjct: 236 KVMANAAASSLKEVTMELGGKSPLIVCEDASLDLAADIAMMANFYSSGQVCTNGTRVFVP 295

Query: 299 SGIYERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGG 358
           + +   F+EK+L R   I  GD   E    GP+ S    DN L YIE GKQEGA LL GG
Sbjct: 296 TRLKAAFEEKILARVARIRPGDLFAESTNFGPLVSFPHRDNVLRYIETGKQEGARLLCGG 355

Query: 359 EKLENGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGL 418
           E L+   +  G +V P +F +   +MTI +EEIFGPV++++  D  EEAL  AN  ++GL
Sbjct: 356 EALKGEGFDRGAWVAPTVFTDCDDQMTIVREEIFGPVMSILSYDDEEEALRRANATEYGL 415

Query: 419 SASIFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFF 478
           +A + T ++ R    I  ++AG+  IN        + P GG K S    RE G      +
Sbjct: 416 AAGVVTPDLNRAHRLIHRLEAGICWINTWGES-PAEMPVGGYKHSGI-GRENGVQTLHSY 473

Query: 479 TAIKTVFVK 487
           T IK++ V+
Sbjct: 474 TQIKSIQVE 482


Lambda     K      H
   0.315    0.132    0.374 

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: 561
Number of extensions: 31
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: 488
Length of database: 490
Length adjustment: 34
Effective length of query: 454
Effective length of database: 456
Effective search space:   207024
Effective search space used:   207024
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 (21.5 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