GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS07615
          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 (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