GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Echinicola vietnamensis KMM 6221, DSM 17526

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate Echvi_1071 Echvi_1071 acetyl-CoA acetyltransferases

Query= BRENDA::P45359
         (392 letters)



>FitnessBrowser__Cola:Echvi_1071
          Length = 391

 Score =  290 bits (743), Expect = 4e-83
 Identities = 173/403 (42%), Positives = 248/403 (61%), Gaps = 31/403 (7%)

Query: 3   EVVIASAVRTAIGSYGKS-LKDVPAVDLGATAIKEAVKKA-GIKPEDVNEVILGNVL-QA 59
           +  I    RTA+G   K   +     DL    IK+ +    G++ E V+++I+GN + +A
Sbjct: 2   DAYIIKGYRTAVGKAKKGGFRFYRPDDLAVDVIKKLIADTPGLEAERVDDLIVGNAVPEA 61

Query: 60  GLGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMS 119
             G    R  S  A L   +P   IN+ CGSGL  ++LA   IK+G AD IIAGG E+MS
Sbjct: 62  EQGMQMGRMISLMA-LGKVVPGFIINRYCGSGLEAIALATAKIKSGMADCIIAGGTESMS 120

Query: 120 RAPYLANNARWGYRMG-NAKFVDEMITDGLWDAFNDYH--MGITAENIAERWNISREEQD 176
             P +      GY+   N K   E           DY+  MG+TAE +A+ ++ISRE+ D
Sbjct: 121 MVPMM------GYKTALNWKIASE---------HPDYYLSMGLTAEELAKDYDISREDSD 165

Query: 177 EFALASQKKAEEAIKSGQFKDEIVPVVIK------GRKGET---VVDTDEHPRFGSTIEG 227
           +FA+ S ++A  AIK G+FK+EIVP+ ++        K +T    VDTDE PR G+ ++ 
Sbjct: 166 QFAVTSHERAISAIKEGRFKEEIVPIEVEETFVDASGKRQTRTFTVDTDEGPRPGTNMDV 225

Query: 228 LAKLKPAFKKDGTVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAI 287
           L  LKPAFK+ G VTAGN+S  +D AA  V+MS    KEL ++P+A++VSY  AGVDP I
Sbjct: 226 LGGLKPAFKQGGQVTAGNSSQTSDGAAFTVVMSERMVKELNLEPVARLVSYSVAGVDPRI 285

Query: 288 MGYGPFYATKAAIEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALG 347
           MG GP  A   A+++AG  + ++ L+E NEAFAAQ+LAV + L  D N VNVNGGA+ALG
Sbjct: 286 MGIGPKEAVPKALKQAGMKMSDISLVELNEAFAAQALAVIRALDMDPNTVNVNGGAVALG 345

Query: 348 HPIGASGARILVTLVHAMQKRDAKKGLATLCIGGGQGTAILLE 390
           HP+G +GA++ V +++ +++R+ K G+ T C+GGGQG A ++E
Sbjct: 346 HPLGCTGAKLTVQMINELRRRNQKYGMVTACVGGGQGVAGVVE 388


Lambda     K      H
   0.315    0.132    0.375 

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: 429
Number of extensions: 27
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: 392
Length of database: 391
Length adjustment: 31
Effective length of query: 361
Effective length of database: 360
Effective search space:   129960
Effective search space used:   129960
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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