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_RS07615 BWI76_RS07615 betaine-aldehyde dehydrogenase

Query= curated2:Q12QD2
         (498 letters)



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

 Score =  201 bits (512), Expect = 4e-56
 Identities = 152/459 (33%), Positives = 226/459 (49%), Gaps = 15/459 (3%)

Query: 12  QTQFIAGQWL-AGKGPSFSSVNPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSLT 70
           Q  +I G ++ A  G +F ++NPANGEV+     A    VD A+ SA+     W+AMS  
Sbjct: 7   QQLYIDGGYVSATSGKTFETINPANGEVLATVQAAGREDVDRAVKSAQKGQKIWAAMSAM 66

Query: 71  ERLVIVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKANA--ERTG 128
           ER  I+    + L+   +  AR   L+TGK L E+   V  +TG   +   A       G
Sbjct: 67  ERSRILRKAVDILRARNDELARLETLDTGKPLSETAA-VDIVTGADVLEYYAGLIPALEG 125

Query: 129 TVENPMPGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVA 188
           +       +  + R +P GVVA  G +N+P  +      PAL AGN ++FKPSE+TP  A
Sbjct: 126 SQIPLRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTPLTA 185

Query: 189 ELTMQLWQQAGLPNGVLNLLQGEIA-TGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQP 247
               +++++AGLP GV N+L G  A TG+ L  H  I  + FTG   +G  +    A   
Sbjct: 186 LKLAEIYREAGLPAGVFNVLPGTGAETGQYLTEHPDIAKISFTGGVASGKKVMANAAASS 245

Query: 248 GKILALEMGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILA 307
            K + +E+GG +PLI+ E A++D A    + + F SSGQ CT   R+F+P T    A   
Sbjct: 246 LKEVTMELGGKSPLIVCEDASLDLAADIAMMANFYSSGQVCTNGTRVFVP-TRLKAAFEE 304

Query: 308 KLLTSTAKIALGDPFAETQPFFGAMISDKAAAGMVKAQADIQAAGGVSLIELTQVTPGLG 367
           K+L   A+I  GD FAE+   FG ++S      +++   +     G  L+   +   G G
Sbjct: 305 KILARVARIRPGDLFAESTN-FGPLVSFPHRDNVLR-YIETGKQEGARLLCGGEALKGEG 362

Query: 368 F-----VTPGII-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLAD 421
           F     V P +  D  D   +  EE FGP++ +  Y D + A+  AN T +GL+AG++  
Sbjct: 363 FDRGAWVAPTVFTDCDDQMTIVREEIFGPVMSILSYDDEEEALRRANATEYGLAAGVVTP 422

Query: 422 SETDYQHFYRRIRAGIVNWNKPITGASSAAPFGGIGASG 460
                     R+ AGI  W      + +  P GG   SG
Sbjct: 423 DLNRAHRLIHRLEAGIC-WINTWGESPAEMPVGGYKHSG 460


Lambda     K      H
   0.317    0.133    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: 612
Number of extensions: 32
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: 498
Length of database: 490
Length adjustment: 34
Effective length of query: 464
Effective length of database: 456
Effective search space:   211584
Effective search space used:   211584
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 (21.7 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