GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Streptomyces kebangsaanensis SUK12

Align Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase

Query= SwissProt::Q8GAI8
         (450 letters)



>NCBI__GCF_001906585.1:WP_073950325.1
          Length = 511

 Score =  290 bits (742), Expect = 7e-83
 Identities = 181/443 (40%), Positives = 249/443 (56%), Gaps = 6/443 (1%)

Query: 4   TLASATSEDAVAALEAACAAQTSWARTAPRVRAEILRRAFDLVTARSEDFALLMTLEMGK 63
           T   A  +D  AA+ AA  A   WA   P  R++ L R  +++  R+EDFA   +L+ GK
Sbjct: 51  TYELAGPDDVDAAVAAAREAFPGWAGATPGDRSDALHRFAEVLADRAEDFARAESLQCGK 110

Query: 64  PLAEARG-EVAYGAEFLRWFSEETVRDYGRYLTTPEGKNKILVQHKPVGPCLLITPWNFP 122
           PL   R  +V    +   +F+       G+      G +   V+ +P+G    I PWN+P
Sbjct: 111 PLKLTREFDVPGTIDNAAFFAGAARHLQGQSAGEYSGDHTSYVRREPIGVVGSIAPWNYP 170

Query: 123 LAMATRKVAPAVAAGCTMVLKPAKLTPLTSQLFAQTMMEAGLPAGVLNVVSSSSASGISG 182
           L MA  KV PA+AAG T+VLKPA+LTPLTS LFAQ   EAG+P GV+N+V+ +       
Sbjct: 171 LQMAAWKVLPAIAAGNTIVLKPAELTPLTSLLFAQAATEAGIPDGVINIVTGTGKEA-GE 229

Query: 183 PLLKDSRLRKVSFTGSTPVGKRLMSDASRHVLRTSMELGGNAPFVVFEDADLDKAVEGAM 242
            L+    +  VSFTGST VGKR+   A+  V R  +ELGG APFVVF+DADL+ AV GA+
Sbjct: 230 HLVGHPDVAMVSFTGSTAVGKRVAEIATASVKRLHLELGGKAPFVVFDDADLEAAVNGAV 289

Query: 243 AAKMRNMGEACTAANRFLVQESVAQEFTRKFAAAMGALSTGRGTDPASQVGPLINNGARD 302
           A  + N G+ CTAA R  VQ  + +EF  + AA M  +  G    P + +GPLI++  RD
Sbjct: 290 AGALINTGQDCTAATRAYVQRPLYEEFVARTAALMETVRLGDPFAPGTDLGPLISHVHRD 349

Query: 303 DIHALVTAAVDAGAVAVTGGAPVDGP---GYFYQPTVLADVPNNAAILGQEIFGPVAPVT 359
            +   V  A  A A  VTGG    G    G +Y+PT++A    ++ I+  EIFGPV  V 
Sbjct: 350 RVAGFVDRA-RAYARVVTGGEAPQGELKNGAYYRPTLIAGAAQDSEIVQSEIFGPVLVVL 408

Query: 360 TFTTEQDAIKLANASEYGLAAYLYSRDFNRLLRVAEQIEFGMVGFNAGIISNAAAPFGGV 419
            F ++ + I+LAN + YGLAA  +SRD  R  R   +I+ G V  N  I   +  P GG 
Sbjct: 409 PFDSDDEGIRLANDTAYGLAASAWSRDVYRANRATREIKAGCVWVNDHIPIISEMPHGGS 468

Query: 420 KQSGLGREGGSEGIAEYTTTQYI 442
           KQSG G++  S    EYT  +++
Sbjct: 469 KQSGFGKDMSSYSFEEYTQIKHV 491


Lambda     K      H
   0.317    0.131    0.376 

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: 472
Number of extensions: 23
Number of successful extensions: 4
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: 450
Length of database: 511
Length adjustment: 34
Effective length of query: 416
Effective length of database: 477
Effective search space:   198432
Effective search space used:   198432
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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