GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Pseudomonas fluorescens FW300-N2E2

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate Pf6N2E2_4679 Betaine aldehyde dehydrogenase (EC 1.2.1.8)

Query= BRENDA::P49419
         (539 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4679
          Length = 490

 Score =  218 bits (556), Expect = 3e-61
 Identities = 139/454 (30%), Positives = 232/454 (51%), Gaps = 13/454 (2%)

Query: 71  PANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALREKIQVLGS 130
           PAN E +A+V++A+  D E  V  A +  K+WA + A +R  I+R+  D LRE+   L +
Sbjct: 29  PANGEVLAQVQRATFEDVERAVVSAEKGQKVWAAMTAMQRSRILRRAVDILRERNDELAA 88

Query: 131 LVSLEMGKILVEG-VGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQWNPVGLVG 189
           L +L+ GK   E    ++    D+ +Y  GL   I G  +P   +      +  P+G+V 
Sbjct: 89  LETLDTGKAYSETRYVDIVTGTDVLEYYAGLVPAIEGEQIPLRDTSFVYTRR-EPLGVVA 147

Query: 190 IITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLEDNKLPGAICS 249
            I A+N+P+ +  W +A A+  GN  ++K +  TSL ++ + +I     E    PG    
Sbjct: 148 GIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTLKLAEIYT---EAGVPPGVFNV 204

Query: 250 LTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSL-LELGGNNAIIAFED 308
           LT  G ++GT + +  R+  +SFTG T  GK+V         + + +ELGG + +I F+D
Sbjct: 205 LTGSGREVGTWLTEHPRIEKVSFTGGTDTGKKVMASASSSSLKDVTMELGGKSPLIIFDD 264

Query: 309 ADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIRVGNPWDPNVL 368
           ADL     +A+ A   ++GQ CT   R+F+   +      ++ +  A+IR+GNP D N  
Sbjct: 265 ADLDRAADTAMMANFYSSGQVCTNGTRVFVPSHLKAAFEAKIAERVARIRIGNPEDENTN 324

Query: 369 YGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMD----RPGNYVEPTIVTGLGHDASIA 424
           +GPL +   +   LG +E+ K EG  ++ GG  +       G +V PT+ T    + +I 
Sbjct: 325 FGPLVSFAHMESVLGYIEKGKAEGARLLCGGNRLTDGELAKGAFVAPTVFTDCTDEMTIV 384

Query: 425 HTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCGIVNVN 484
             E F P++ +  ++ EEEV    N+   GL++ + T+DL R  R +     + GI  +N
Sbjct: 385 REEIFGPVMSILTYETEEEVIRRANDTDFGLAAGVVTRDLNRAHRVI--HQLEAGICWIN 442

Query: 485 IPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMR 518
                ++     GG K +G GRE+G  +   + R
Sbjct: 443 -AWGESDAKMPVGGYKQSGVGRENGISSLNNFTR 475


Lambda     K      H
   0.318    0.136    0.417 

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: 649
Number of extensions: 38
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: 539
Length of database: 490
Length adjustment: 35
Effective length of query: 504
Effective length of database: 455
Effective search space:   229320
Effective search space used:   229320
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 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