GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Klebsiella michiganensis M5al

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate BWI76_RS07615 BWI76_RS07615 betaine-aldehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS07615 BWI76_RS07615
           betaine-aldehyde dehydrogenase
          Length = 490

 Score =  252 bits (644), Expect = 2e-71
 Identities = 167/489 (34%), Positives = 252/489 (51%), Gaps = 28/489 (5%)

Query: 36  EYPLIINGERV--TTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVN 93
           E  L I+G  V  T+    ++ NPA   +++ +V  A ++  ++A++SA +  + W  ++
Sbjct: 6   EQQLYIDGGYVSATSGKTFETINPAN-GEVLATVQAAGREDVDRAVKSAQKGQKIWAAMS 64

Query: 94  PEERANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADA-DTAEAIDFLEYYARQMIELN 152
             ER+ IL KA  I+R R  E +     + GKP  E  A D     D LEYYA  +I   
Sbjct: 65  AMERSRILRKAVDILRARNDELARLETLDTGKPLSETAAVDIVTGADVLEYYAG-LIPAL 123

Query: 153 RGKEILSRPGEQNRYFYT---PMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPAST 209
            G +I   P   + + YT   P+GV   I  WN+ + I +  +   +  GN ++ KP+  
Sbjct: 124 EGSQI---PLRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEV 180

Query: 210 TPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYER 269
           TP+ A K  E+  +AGLP GV N +PG+GAE G YL +HP  + I+FTG    G ++   
Sbjct: 181 TPLTALKLAEIYREAGLPAGVFNVLPGTGAETGQYLTEHPDIAKISFTGGVASGKKVMAN 240

Query: 270 AAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIH 329
           AA      + LK V +E+GGK  ++V  DA LDLAA+  +++ F  SGQ C+ G+R  + 
Sbjct: 241 AAA-----SSLKEVTMELGGKSPLIVCEDASLDLAADIAMMANFYSSGQVCTNGTRVFVP 295

Query: 330 KDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGG 388
             +     EK +A    +  GD        GP++     + ++ YIE GK+EG RL+ GG
Sbjct: 296 TRLKAAFEEKILARVARIRPGDLFAESTNFGPLVSFPHRDNVLRYIETGKQEGARLLCGG 355

Query: 389 EGDSSTGF----FIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGL 444
           E     GF    ++ PT+  D D +  I++EEIFGPV++    +D + AL  AN TEYGL
Sbjct: 356 EALKGEGFDRGAWVAPTVFTDCDDQMTIVREEIFGPVMSILSYDDEEEALRRANATEYGL 415

Query: 445 TGAVIT--RNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYL 502
              V+T   NRAH  +       G  +   N  G      P GG+K SG   +  G   L
Sbjct: 416 AAGVVTPDLNRAH--RLIHRLEAGICWI--NTWGESPAEMPVGGYKHSGI-GRENGVQTL 470

Query: 503 ALHMQAKTV 511
             + Q K++
Sbjct: 471 HSYTQIKSI 479


Lambda     K      H
   0.316    0.134    0.388 

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: 563
Number of extensions: 31
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: 515
Length of database: 490
Length adjustment: 34
Effective length of query: 481
Effective length of database: 456
Effective search space:   219336
Effective search space used:   219336
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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