GapMind for catabolism of small carbon sources

 

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

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein

Query= reanno::WCS417:GFF5420
         (497 letters)



>NCBI__GCF_000828635.1:WP_041097806.1
          Length = 479

 Score =  318 bits (816), Expect = 2e-91
 Identities = 193/475 (40%), Positives = 266/475 (56%), Gaps = 17/475 (3%)

Query: 23  YINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQRAVENARATFNSGVWSRLAPAK 82
           YI+G++ +     T E  SP DG LLATV   +AADA +AV  AR  F++  WS    A+
Sbjct: 8   YIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDA--WSVTPAAE 65

Query: 83  RKSAMLRFAALLKANAEELALLETLDMGKPISDSLNIDVPGAANALS-WSGEAIDKIYDE 141
           R + + +    LKA A+E+A   TL+MG P   S  I V     +   +S    D  ++E
Sbjct: 66  RAAYLKKIQESLKARADEIAKTITLEMGMPYKFSQRIQVGSPTASFGMYSKMLADFPFEE 125

Query: 142 VAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAI 201
                      V RE VGVV AI PWN+PL     K+  AL+ G +V+LKPSE +PL A 
Sbjct: 126 KVGNSK-----VVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPLNAF 180

Query: 202 RIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTLVFTGSTKIAKQLLIRSGESNM 261
            +A +   AG+P GVFN++ GYG  VG A+  H +VD + FTGST+ A   +     + +
Sbjct: 181 LLAEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTR-AGTRVSELASATV 239

Query: 262 KRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPL 321
           KRV LE GGKS  I+  DA D   A +   G    N G+ CTA +R+LV  +   +   L
Sbjct: 240 KRVALELGGKSAAIILDDA-DFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYAEAAKL 298

Query: 322 VIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHADGAKLVAGGKRTLE--ETG 379
            +EA + ++ G+P+     +G L    Q + V  YI  G A+G +L+ GG    E     
Sbjct: 299 AVEAAQAYRVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTGGADLPEGVNPD 358

Query: 380 GTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIANDTIYGLAAAVWTADIS 439
           G YV+PTIF  V     IA+EEIFGPVLS+I++   E+AV+IAN T+YGLA  VW+A   
Sbjct: 359 GYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWSATDE 418

Query: 440 KAHLTAKALRAGSVWVNQYDGG--DMTAPFGGFKQSGNGRDKSLHAFDKYTELKA 492
            A   A+ +R G V +N   GG  +M APFGG+KQSGNGR+   +  + + E KA
Sbjct: 419 HAEQVARRMRTGQVEIN---GGTFNMYAPFGGYKQSGNGRELGKYGLEDFLEFKA 470


Lambda     K      H
   0.316    0.132    0.386 

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: 560
Number of extensions: 29
Number of successful extensions: 7
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: 497
Length of database: 479
Length adjustment: 34
Effective length of query: 463
Effective length of database: 445
Effective search space:   206035
Effective search space used:   206035
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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