GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Herbaspirillum seropedicae SmR1

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate HSERO_RS05395 HSERO_RS05395 succinate-semialdehyde dehdyrogenase

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__HerbieS:HSERO_RS05395
          Length = 484

 Score =  325 bits (832), Expect = 3e-93
 Identities = 174/461 (37%), Positives = 267/461 (57%), Gaps = 1/461 (0%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           +++GQ+        + V NPA   ++  +P   A + R+AI+AA  A P W+   A ER+
Sbjct: 15  FVNGQWCDADQGERLAVHNPANGELLGHVPLMGAAETRRAIEAANAAWPAWKKKTAKERS 74

Query: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129
           + LR+    +     +++ ++  E GK    A  E+ + A +I++ AE  +R  G+ I S
Sbjct: 75  AILRRWYELMLANTDDLALIMTAEQGKPLAEARGEIGYAASFIEWFAEEGKRTYGDTIPS 134

Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189
             P   I++ K A+GV   I PWNFP  +I RK  PAL  G  +V+KP+E TP +A+A A
Sbjct: 135 PSPSNRIVVIKEAIGVCAAITPWNFPAAMITRKAGPALAAGCPMVLKPAEATPFSALALA 194

Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249
            + +  G+P GVF++V G  + +G E+  NP V  +S TGS   G+ +M  +A +I K+ 
Sbjct: 195 VLAERAGIPAGVFSVVTGTPKGIGGEMTSNPIVRKISFTGSTGVGKLLMQQSASSIKKLS 254

Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309
           LELGG AP IV DDADL+ AV+  + S+  N+GQ C CA R+YVQ G+YD F  +L EA+
Sbjct: 255 LELGGNAPFIVFDDADLDAAVEGAIASKYRNAGQTCVCANRIYVQDGVYDAFAAKLVEAV 314

Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369
           +  + G   E   +  GPLIN  A+++VEQ VA AV +GARV  GGK       ++ PT+
Sbjct: 315 KKFKVGQGTEEG-VTQGPLINEQAVQKVEQHVADAVAKGARVLLGGKRHALGHSFFEPTV 373

Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429
           L DV   M +  EETFGP+ P+  F T E+ +++AND+++GL S  Y++++    +  +G
Sbjct: 374 LADVTPAMQVAREETFGPMAPLFRFKTDEEVLALANDTEFGLASYFYSRDIGRIWRVAEG 433

Query: 430 LKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYL 470
           L+ G   IN            G ++SG+G     +G+ +YL
Sbjct: 434 LESGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYL 474


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: 538
Number of extensions: 25
Number of successful extensions: 3
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: 484
Length adjustment: 34
Effective length of query: 445
Effective length of database: 450
Effective search space:   200250
Effective search space used:   200250
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