GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Pseudomonas simiae WCS417

Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate GFF1165 PS417_05920 gamma-aminobutyraldehyde dehydrogenase

Query= SwissProt::Q9H2A2
         (487 letters)



>FitnessBrowser__WCS417:GFF1165
          Length = 474

 Score =  322 bits (826), Expect = 1e-92
 Identities = 175/462 (37%), Positives = 263/462 (56%), Gaps = 11/462 (2%)

Query: 28  YDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERSRVLNQVADLLEQSLEEF 87
           ++P+ G V   +  + + +++AAV+AA  AF SWS  +P++RS +L ++AD++E   EE 
Sbjct: 22  FNPALGRVLVEINEASEAQVDAAVRAADAAFESWSQTAPKDRSLLLLKLADVIEAHGEEL 81

Query: 88  AQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECTQMDHLGCMHYTVRAPVGV 147
           AQ ES + GK  + A   +IP     FRFFA +S   +         G      R PVGV
Sbjct: 82  AQLESDNCGKPYSAALNDEIPAIADVFRFFAGASRCMSGSAGGEYLPGHTSMIRRDPVGV 141

Query: 148 AGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWMLCKLLDKAGVPPGVVNIV 207
              I+PWN PL ++ WKIAPA+AAGNTV+ KPSE T +TA  + +L      P GV+N+V
Sbjct: 142 IASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSEQTPLTALRMVELAADL-FPAGVLNLV 200

Query: 208 FGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLSLELGGKNPAIIFEDAN 267
           FG GP VG  LV+HP+V ++S TGS  T   I   +A   K++ +ELGGK P IIF DA+
Sbjct: 201 FGRGPTVGSPLVNHPKVRMVSLTGSIATGANIISSTADSVKRMHMELGGKAPVIIFSDAD 260

Query: 268 LDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFVEATRKWKVGIPSDPLVSIG 327
           +D  +       F N G+ C    RI+ Q  IY +F+++   A    K G+  DP   +G
Sbjct: 261 IDAAVEGIRTFGFYNAGQDCTAACRIYAQAEIYEQFVEKLGAAVASIKYGLQDDPATELG 320

Query: 328 ALISKAHLEKVRSYVKRALAEG--AQIWCGEGVDKLSLPARNQAGYFMLPTVITDIKDES 385
            LI+  H ++V  +V+RA+A+     +  G+ V+          G+F  PTV+ D + + 
Sbjct: 321 PLITAQHRDRVAGFVERAVAQSHIRLVTGGKAVE--------GNGFFFEPTVLADAQQDD 372

Query: 386 CCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNVGRVHRVAKKLQSGLVWT 445
             +  E+FGPV  V  F  E +V+  AN+  YGLA++VW+++VGR HR+A +LQ G  W 
Sbjct: 373 EIVRREVFGPVVSVTRFTDEAQVLGWANDSDYGLASSVWTADVGRAHRLAARLQYGCTWV 432

Query: 446 NCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITVKH 487
           N   +    +P GG K SG G++ +    + +T ++ +  KH
Sbjct: 433 NTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTSVRHVMFKH 474


Lambda     K      H
   0.319    0.133    0.404 

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: 518
Number of extensions: 16
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: 487
Length of database: 474
Length adjustment: 34
Effective length of query: 453
Effective length of database: 440
Effective search space:   199320
Effective search space used:   199320
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 (21.8 bits)
S2: 51 (24.3 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