GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Sulfuritalea hydrogenivorans sk43H DSM 22779

Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein

Query= curated2:Q12QD2
         (498 letters)



>NCBI__GCF_000828635.1:WP_041097806.1
          Length = 479

 Score =  203 bits (517), Expect = 1e-56
 Identities = 157/471 (33%), Positives = 233/471 (49%), Gaps = 22/471 (4%)

Query: 12  QTQF-IAGQWLAGKGPSFSSV-NPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSL 69
           +TQF I GQW++  G     V +P +G ++      +A   D A+T+AR AF  WS    
Sbjct: 4   RTQFYIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDAWSVTPA 63

Query: 70  TERLVIVEAFAEQLKEHAELFARTIALETGKAL-WESRTEVGAMTGKIAISIKANAERTG 128
            ER   ++   E LK  A+  A+TI LE G    +  R +VG+ T    +  K  A+   
Sbjct: 64  AERAAYLKKIQESLKARADEIAKTITLEMGMPYKFSQRIQVGSPTASFGMYSKMLADFP- 122

Query: 129 TVENPMPGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVA 188
             E  +  +K  +  +  GVVA   P+N+P H     +  AL AG TV+ KPSE+ P  A
Sbjct: 123 -FEEKVGNSK--VVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPLNA 179

Query: 189 ELTMQLWQQAGLPNGVLNLLQG-EIATGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQP 247
            L  ++   AG+P GV NL+ G     G+A+ +H+ +D + FTGS+  G  +  + A   
Sbjct: 180 FLLAEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTRAGTRV-SELASAT 238

Query: 248 GKILALEMGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILA 307
            K +ALE+GG +  II + A+ + AV  ++ + +++SGQ CT   R+ +P T   +A  A
Sbjct: 239 VKRVALELGGKSAAIILDDADFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYAEA--A 296

Query: 308 KLLTSTAK-IALGDPFAE---TQPFFGAMISDKAA--AGMVKAQADIQAAGGVSLIELTQ 361
           KL    A+   +GDP AE     P    M  D+     G   A+      GG  L E   
Sbjct: 297 KLAVEAAQAYRVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTGGADLPE--G 354

Query: 362 VTPGLGFVTPGII-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLA 420
           V P   +V P I   V   S +A EE FGP+L +  Y D + A+  AN T +GL+ G+ +
Sbjct: 355 VNPDGYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWS 414

Query: 421 DSETDYQHFYRRIRAGIVNWNKPITGASSAAPFGGIGASGNHRASAYYAAD 471
            ++   +   RR+R G V  N      +  APFGG   SGN R    Y  +
Sbjct: 415 ATDEHAEQVARRMRTGQVEINGGT--FNMYAPFGGYKQSGNGRELGKYGLE 463


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: 561
Number of extensions: 33
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: 498
Length of database: 479
Length adjustment: 34
Effective length of query: 464
Effective length of database: 445
Effective search space:   206480
Effective search space used:   206480
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 Apr 09 2024. 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