GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Pseudomonas fluorescens FW300-N1B4

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate Pf1N1B4_1734 Succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16)

Query= BRENDA::P49419
         (539 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1734
          Length = 480

 Score =  236 bits (601), Expect = 2e-66
 Identities = 147/465 (31%), Positives = 242/465 (52%), Gaps = 12/465 (2%)

Query: 56  NGSW--GGRGEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEI 113
           +G+W     G+ I    PA  E +  V +   A+    ++ A +A   W  + A +R   
Sbjct: 16  DGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRGLTAKERANK 75

Query: 114 VRQIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSER 173
           +R+  + + E    L  L++LE GK L E  GE+       ++    ++ + G ++P  +
Sbjct: 76  LRRWFELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRVYGDVIPGHQ 135

Query: 174 SGHALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKI 233
               LI    P+G+   IT +NFP A+       A+  G   + K A  T   + A    
Sbjct: 136 PDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFA---- 191

Query: 234 IAKVLEDNKLPGAICSLTCGGA-DIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGR 292
           +A++ +   +P  + S+  G A DIG+ +  +  V  LSFTGST++G+Q+     +   +
Sbjct: 192 LAELAQRAGIPNGVFSVVTGSAGDIGSELTGNPIVRKLSFTGSTEIGRQLMTECAKDIKK 251

Query: 293 SLLELGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKK 352
             LELGGN   I F+DADL   V  A+ +     GQ C  A RL+I +S++D    +LK 
Sbjct: 252 VSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVYDAFAEKLKV 311

Query: 353 AYAQIRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPT 412
           A A++++GN  +     GPL  ++AV+     + +A  +G TV+ GGK M   GN+ EPT
Sbjct: 312 AVAKLKIGNGLEDGTTTGPLIDEKAVAKVQEHIADAVGKGATVLAGGKSMQ--GNFFEPT 369

Query: 413 IVTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLG 472
           I+T + ++A++A  ETF P+  +F+FK+E +V A +N+ + GL+S  + +DLGR+FR   
Sbjct: 370 ILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFR--V 427

Query: 473 PKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517
            +  + G+V VN      E+   FGG K +G GRE      + Y+
Sbjct: 428 AEALEYGMVGVNTGLISNEV-APFGGIKASGLGREGSKYGIEDYL 471


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: 678
Number of extensions: 29
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: 539
Length of database: 480
Length adjustment: 34
Effective length of query: 505
Effective length of database: 446
Effective search space:   225230
Effective search space used:   225230
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