GapMind for catabolism of small carbon sources

 

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

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate Pf1N1B4_4931 Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20); Succinate-semialdehyde dehydrogenase [NADP+] (EC 1.2.1.79)

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4931
          Length = 485

 Score =  342 bits (878), Expect = 1e-98
 Identities = 181/468 (38%), Positives = 283/468 (60%), Gaps = 2/468 (0%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           Y+DGQ++     A +DV++PA+  +++R+P  Q    R+AI+AAERA P W A PA ERA
Sbjct: 17  YVDGQWIGADNAATLDVIDPASGQLLARVPAMQGAQTRRAIEAAERAWPAWRARPAAERA 76

Query: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129
           + L +    + +   +++ ++  E GK    A+ E+ + A ++ + AE ARR  GE + +
Sbjct: 77  ALLERWYQAMIDNLDDLALIMTCEQGKPLNEAKGEIRYGAGFVKWFAEEARRVYGETMPA 136

Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189
                 +L  K+ +GV   I PWNFP  +I RK APAL  G  I++KPS+ TP +A+A A
Sbjct: 137 PSGDRRLLTLKQPVGVCAAITPWNFPNAMITRKCAPALAAGCPIIVKPSDLTPLSALALA 196

Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249
            + + +G+P GVFN++ G    +G+EL GNP V  +S TGS + G  +M  +A++I ++ 
Sbjct: 197 VLAERVGIPAGVFNVLTGMPAGIGEELTGNPTVRKISFTGSTAVGRLLMRQSAEHIKRLS 256

Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309
           LELGG AP IV DDADLE AV  I+ S+  N+GQ C CA R+ VQ GIY++F  RL E +
Sbjct: 257 LELGGNAPFIVFDDADLEQAVAGIMLSKFRNAGQTCVCANRILVQDGIYERFAQRLVEEV 316

Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369
             ++ GN  +  D+ +GPLIN AA+ ++ + +  A+ +GAR+  GG   EG   +  PT+
Sbjct: 317 GKLKVGNGLDA-DVTIGPLINPAAVSKIARHIDDALSQGARLLCGG-IPEGDSQFVQPTV 374

Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429
           L D    M + +EETFGPV P++ F    +A+++AN + YGL +  +TQ+L  + +  + 
Sbjct: 375 LGDTHAGMLLANEETFGPVAPLMRFTDEAEALALANATPYGLGAYYFTQDLRRSWRFGEA 434

Query: 430 LKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477
           L+FG   +N            G ++SG+G    K+GL EYL+ +  ++
Sbjct: 435 LEFGMVGLNTGIISMEVAPFGGIKQSGLGREGSKYGLDEYLEVKAFHI 482


Lambda     K      H
   0.318    0.135    0.392 

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: 583
Number of extensions: 31
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: 479
Length of database: 485
Length adjustment: 34
Effective length of query: 445
Effective length of database: 451
Effective search space:   200695
Effective search space used:   200695
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