GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pseudomonas fluorescens FW300-N2E3

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate AO353_11505 AO353_11505 succinate-semialdehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_11505
          Length = 480

 Score =  339 bits (869), Expect = 1e-97
 Identities = 177/468 (37%), Positives = 278/468 (59%), Gaps = 3/468 (0%)

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

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

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

Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249
           ++    G+P+GV ++V G    +G EL  NP V  +S TGS   G ++MA  AK+I KV 
Sbjct: 194 ELAQRAGIPKGVLSVVTGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMAECAKDIKKVS 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  E      GPLI+  A+ +V++ +A A+ +GA +  GGK +EG   ++ PT+
Sbjct: 314 AKLKIGNGLEEG-TTTGPLIDGKAVAKVQEHIADALSKGATLLAGGKVMEGN--FFEPTI 370

Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429
           L +V +  ++  EETFGP+ P+  F    + I+M+ND+++GL S  Y ++L    +  + 
Sbjct: 371 LTNVPKSAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDLGRVFRVAEA 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: 552
Number of extensions: 20
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 (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