GapMind for catabolism of small carbon sources

 

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

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein

Query= BRENDA::Q72IB9
         (516 letters)



>NCBI__GCF_000828635.1:WP_041097806.1
          Length = 479

 Score =  239 bits (611), Expect = 1e-67
 Identities = 164/485 (33%), Positives = 237/485 (48%), Gaps = 28/485 (5%)

Query: 41  YIGGEWVDTK-ERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRS 99
           YI G+WV    +  + +       ++ T  +   A+A+ A+ AA  AF  W   P  +R+
Sbjct: 8   YIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDAWSVTPAAERA 67

Query: 100 RLLLKAAALMRRRKRELEATLVYEVGKNW-VEASADVAEAIDFIEYYARAALRYRYPAVE 158
             L K    ++ R  E+  T+  E+G  +       V         Y++    +      
Sbjct: 68  AYLKKIQESLKARADEIAKTITLEMGMPYKFSQRIQVGSPTASFGMYSKMLADF------ 121

Query: 159 VVPYPGEDNESFYVPLGAGVV--IAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVG 216
             P+  +   S  V    GVV  I PWN+P+      +   +A G TV+ KP+E A +  
Sbjct: 122 --PFEEKVGNSKVVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPLNA 179

Query: 217 AKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLA 276
             + EI H AG P GV N + G G  VG  +V H     ++FTGS   G ++ E A    
Sbjct: 180 FLLAEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTRAGTRVSELASATV 239

Query: 277 PGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYE 336
                 KR  +E GGK A I+ + ADF++A +GVV + Y   GQ C+A +R+++    Y 
Sbjct: 240 ------KRVALELGGKSAAIILDDADFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYA 293

Query: 337 PVLERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRL-E 393
              +  ++ A+   VG P  E   LGP+ S  Q+ +V  YI  G  EG +L+ GG  L E
Sbjct: 294 EAAKLAVEAAQAYRVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTGGADLPE 353

Query: 394 G---EGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVY 450
           G   +GY++ PT+F +V P + IAQEEIFGPVLS+I   D  +A+ +AN T YGL GGV+
Sbjct: 354 GVNPDGYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVW 413

Query: 451 SRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMK 510
           S   EH E   R    G +  N    G      PFGG+K SG   + G    L  FLE K
Sbjct: 414 SATDEHAEQVARRMRTGQVEIN---GGTFNMYAPFGGYKQSGNGRELGKYG-LEDFLEFK 469

Query: 511 AVAER 515
           A+  R
Sbjct: 470 AMQFR 474


Lambda     K      H
   0.319    0.137    0.403 

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: 598
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: 516
Length of database: 479
Length adjustment: 34
Effective length of query: 482
Effective length of database: 445
Effective search space:   214490
Effective search space used:   214490
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 (21.7 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