GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Pseudomonas fluorescens FW300-N2C3

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate AO356_10720 AO356_10720 succinate-semialdehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10720 AO356_10720
           succinate-semialdehyde dehydrogenase
          Length = 480

 Score =  338 bits (867), Expect = 2e-97
 Identities = 179/468 (38%), Positives = 278/468 (59%), Gaps = 3/468 (0%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           +IDG +V       I V NPAT  V+  +P   A + R+AI+AA++A P W AL A ERA
Sbjct: 14  FIDGAWVDADNGQTIKVTNPATGEVLGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73

Query: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129
           + LR+    + E   ++  L+  E GK    A+ E+ + A +I++ AE A+R  G++I  
Sbjct: 74  NKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGDVIPG 133

Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189
            +P + +++ K+ +GVT  I PWNFP  +I RK  PAL  G T+VIKP+  TP +A+A  
Sbjct: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQTPFSALALV 193

Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249
           ++    G+P+GV ++V G    +G EL  NP V  +S TGS   G ++MA  AK+I KV 
Sbjct: 194 ELAHRAGIPQGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQLMAECAKDIKKVS 253

Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309
           LELGG AP IV DDADL+ AV+  + S+  N+GQ C CA R+Y+Q  +YD F  +L  A+
Sbjct: 254 LELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVYDAFAEKLKVAV 313

Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369
             ++ GN  + +    GPLI+  A+ +V++ +A AV +GA V  GGKA+EG   ++ PT+
Sbjct: 314 AKLKIGNGLD-DGTTTGPLIDGKAVAKVQEHIADAVSKGATVLSGGKAMEGN--FFEPTI 370

Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429
           L +V +  ++  EETFGP+ P+  F    + I+M+ND+++GL S  Y ++L    +  + 
Sbjct: 371 LTNVPKNAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDLGRVFRVAEA 430

Query: 430 LKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477
           L++G   +N            G + SG+G    K+G+ +YL+ + + L
Sbjct: 431 LEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478


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: 555
Number of extensions: 17
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: 480
Length adjustment: 34
Effective length of query: 445
Effective length of database: 446
Effective search space:   198470
Effective search space used:   198470
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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