GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Paraburkholderia bryophila 376MFSha3.1

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate H281DRAFT_03540 H281DRAFT_03540 succinate semialdehyde dehydrogenase (EC 1.2.1.16)

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__Burk376:H281DRAFT_03540
          Length = 479

 Score =  327 bits (839), Expect = 4e-94
 Identities = 186/468 (39%), Positives = 274/468 (58%), Gaps = 5/468 (1%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           YI G++  + G +   V+NPAT  VI+++  G A +A +AI AAERA P W +L A ER+
Sbjct: 10  YIGGEW--YEGASTYPVLNPATGEVIAQVAKGGAVEATQAIAAAERAFPAWRSLTAKERS 67

Query: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129
           + +++    + E    ++AL+  E GK    A  EV + A + ++ AE A+R  G++I S
Sbjct: 68  ARVKRWGELMLEHRDALAALLTREQGKPLAEARGEVGYAASFFEWFAEEAKRAYGDVIPS 127

Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189
             P   I++ +  +GV   I PWNFP  +I RK  PAL  G T+V+KPSE TP +A+A A
Sbjct: 128 PNPNAKIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETPLSALALA 187

Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249
            + ++ G+P GVFN+V G    +G  L  +  V  +S TGS   G+ +   +A  + K+ 
Sbjct: 188 VLAEKAGIPPGVFNVVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSADTLKKLS 247

Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309
           LELGG AP IV DDADL+ AV+  + S+  N+GQ C C  R YVQ GIYD F   L +A 
Sbjct: 248 LELGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFTLALAQAA 307

Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369
           + ++ GN A + D+  GPLIN AAL +VE  VA A+++GA+V  G K     G +Y PT+
Sbjct: 308 RKMRVGN-ALQGDVEQGPLINQAALTKVEAHVADALQKGAKVLTGAKPHALGGTFYEPTV 366

Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429
           L+D    M I  EETFGPV     F T ++A++ AN + +GL++  YT++L  A +  + 
Sbjct: 367 LVDASSSMLIAQEETFGPVAACFRFKTEDEAVAAANATPFGLSAYFYTRDLARAWRVGEA 426

Query: 430 LKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477
           L+ G   IN            G ++SG+G    K+GL EY  T++ Y+
Sbjct: 427 LESGMVGINEGILSTEVAPFGGVKQSGLGREGSKYGLDEY--TELKYM 472


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: 530
Number of extensions: 17
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 479
Length of database: 479
Length adjustment: 34
Effective length of query: 445
Effective length of database: 445
Effective search space:   198025
Effective search space used:   198025
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