GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Klebsiella michiganensis M5al

Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate BWI76_RS10695 BWI76_RS10695 aldehyde dehydrogenase PuuC

Query= curated2:Q9AAL5
         (472 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS10695 BWI76_RS10695 aldehyde
           dehydrogenase PuuC
          Length = 495

 Score =  199 bits (505), Expect = 2e-55
 Identities = 148/450 (32%), Positives = 221/450 (49%), Gaps = 20/450 (4%)

Query: 10  DPYTGEAIADFAVNDARSIDAACHSARAAF--AEWAMTPLAERRAIALRFAETVRARREE 67
           DP   + +A+ A      +D A  +AR  F   +W+    A+R+A+  +FA+ + A REE
Sbjct: 41  DPAAQQTLAEVARGKKADVDRAVQAARGVFDRGDWSQASPAQRKAVLTKFADLMDAHREE 100

Query: 68  IATLIARETGKPMWEALTEADSVAAK-VAISIRAQDERAGERSEPMADATARLAHRPHGV 126
           +A L   +TGKP+  +L +    AA+ +     A D+  GE +    +  A +   P GV
Sbjct: 101 LALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVAPTGGNELAMIVREPIGV 160

Query: 127 LAVIGPFNFPMHLANGHIVPALLAGNAVVFKPSEKTPACGQLMGELWRAAGLPDHVLTIV 186
           +A + P+NFP+ LA   + PAL +GN+VV KPSEK+P     +  L + AGLPD V  +V
Sbjct: 161 IAAVVPWNFPLLLACWKLGPALASGNSVVLKPSEKSPLTALRLAGLAKQAGLPDGVFNVV 220

Query: 187 IG-GGEAGEALVRHEALDGVLFTGGVQAGRAIHRALADAPHKILALELGG-NAPLVVWDV 244
            G G EAG+AL  H  ++ + FTG  +  + + +   D+  K + LE GG +A +V  D 
Sbjct: 221 SGFGHEAGQALALHPDVEVITFTGSTRTAKQLLKDAGDSNMKRVWLEAGGKSANIVFADC 280

Query: 245 ADIEAAAHLIVQSAYVTAGQRCTCARRLILPEGARGDALLEALTMLMDRLVIGGPFQSPA 304
            D++ A +      +   GQ C    RL+L E    D  L+ L         G P   P 
Sbjct: 281 PDLQKAVNATAGGIFYNQGQVCIAGTRLLLEESI-ADRFLDLLKEQAKGWQPGNPL-DPN 338

Query: 305 PFMGPVID------AHAAAQVLAAQDRMTADGGRPLRLAAVREARSALLSPGLIELTDAP 358
             MG +ID       H+  +   A   +  DG +    AAV       + P       +P
Sbjct: 339 TTMGMLIDNTHADSVHSFIRAGEAHSTLLLDGRKNPWPAAVGPTIFVDVDPA------SP 392

Query: 359 LRDEEIFGPLLQVRRAADFDAALALANATRFGLAAGLISDDEALYRRFWTSVRAGIVNWN 418
           L  EEIFGP+L V R  + + ALALAN +R+GL A + + D +   R    ++AG V  N
Sbjct: 393 LSQEEIFGPVLVVTRFKNEEQALALANDSRYGLGAAVWTRDLSRAHRVSRRLKAGSVFVN 452

Query: 419 RPTTGASSAAPFGGVGGSGNHRPSAYYAAD 448
               G     PFGG   SGN R  + +A +
Sbjct: 453 NYNDG-DMTVPFGGYKQSGNGRDKSLHALE 481


Lambda     K      H
   0.320    0.135    0.400 

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: 579
Number of extensions: 29
Number of successful extensions: 6
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: 472
Length of database: 495
Length adjustment: 34
Effective length of query: 438
Effective length of database: 461
Effective search space:   201918
Effective search space used:   201918
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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