GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Amantichitinum ursilacus IGB-41

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_053938969.1 WG78_RS16670 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>NCBI__GCF_001294205.1:WP_053938969.1
          Length = 466

 Score =  330 bits (846), Expect = 6e-95
 Identities = 172/449 (38%), Positives = 267/449 (59%), Gaps = 1/449 (0%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           +++G ++       + V NPAT  +I+ IP     + R+AI+AA+ A P W +  A ER+
Sbjct: 14  FVNGAWIDADNQETVPVNNPATGEIIAHIPKLGKAETRRAIEAAQAAWPAWRSKTAKERS 73

Query: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129
             LRK +  +     +++ ++  E GK    A  E+ + A YI++ AE ARR EG+II  
Sbjct: 74  QILRKWNDLMLANVDDLALILTSEQGKPLAEARGEITYAASYIEWFAEEARRIEGDIIAP 133

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

Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249
            + +  G+P G+FN++ G    +G EL  +P V  ++ TGS   G K++  +A  I K+ 
Sbjct: 194 VLAERAGVPAGIFNVLTGSSTEIGGELTASPIVRKITFTGSTEVGAKLIEQSAPTIKKMS 253

Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309
           +ELGG AP IV DDADL+ AV+  + S+  NSGQ C CA R+ VQ G+YD F  +L +A+
Sbjct: 254 MELGGNAPFIVFDDADLDAAVQGAIGSKYRNSGQTCVCANRLLVQAGVYDAFAQKLADAV 313

Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369
            A++ GN  + + +  GPLI+  A+ ++E+ +A A  +GA+V  GGK     G ++ PT+
Sbjct: 314 NALKVGNGVD-DGVTQGPLIDDKAIAKIEEHIADATGKGAQVLTGGKRHALGGTFFEPTI 372

Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429
           L  V   M +  EETFGP+ P+  F+T E+AI+MAND+++GL S  YT++L    +  +G
Sbjct: 373 LTGVTPAMKVAREETFGPLAPLFKFETEEEAIAMANDTEFGLASYFYTRDLARIFRVAEG 432

Query: 430 LKFGETYINRENFEAMQGFHAGWRKSGIG 458
           L++G   IN     +      G ++SG+G
Sbjct: 433 LEYGMVGINAGLISSEVAPFGGVKQSGLG 461


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: 554
Number of extensions: 19
Number of successful extensions: 2
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: 466
Length adjustment: 33
Effective length of query: 446
Effective length of database: 433
Effective search space:   193118
Effective search space used:   193118
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 24 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