GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pedobacter sp. GW460-11-11-14-LB5

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate CA265_RS17585 CA265_RS17585 acetyl-CoA acetyltransferase

Query= BRENDA::P45359
         (392 letters)



>FitnessBrowser__Pedo557:CA265_RS17585
          Length = 391

 Score =  288 bits (736), Expect = 2e-82
 Identities = 167/400 (41%), Positives = 247/400 (61%), Gaps = 24/400 (6%)

Query: 3   EVVIASAVRTAIGSYGKSL-KDVPAVDLGATAIKEAVKKA-GIKPEDVNEVILGNVL-QA 59
           E  I +  RTA+G   + + +   A DL A  I+  V     +  E +++VI+GN   +A
Sbjct: 2   EAYIIAGYRTAVGKAPRGVFRFTRADDLAAEVIRALVASVPNLDNEQIDDVIVGNATPEA 61

Query: 60  GLGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMS 119
             G N  R  S       ++P +T+N+ C SGL T++ A   IKAG AD IIAGG+E MS
Sbjct: 62  EQGLNIGRMISLMGLDTDKVPGVTVNRYCASGLDTIATAVAKIKAGMADCIIAGGVEVMS 121

Query: 120 RAPYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFA 179
             P+       G+++     V +   D  W       MG+TAE +A+ +N+SRE+QD F+
Sbjct: 122 GMPF------GGWKLVPNAEVAKNNPDWYWG------MGLTAEAVAKEYNVSREDQDAFS 169

Query: 180 LASQKKAEEAIKSGQFKDEIVPVVI---------KGRKGETVVDTDEHPRFGSTIEGLAK 230
           L S +KA  AIK+G  KD I+P+ +         K +    VVDTDE PR  +T++ LAK
Sbjct: 170 LKSHEKAIHAIKNGHLKDGILPITVNENYLDANLKKKTRSYVVDTDEGPRADTTLDKLAK 229

Query: 231 LKPAFKKDGTVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGY 290
           LKP F   G+VTAGN+S  +D AA ++++S +K KEL  +P+A++VSYG AGV P IMG 
Sbjct: 230 LKPVFDAVGSVTAGNSSQTSDGAAFVLVVSEKKMKELNAEPIARLVSYGIAGVPPRIMGI 289

Query: 291 GPFYATKAAIEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPI 350
           GP  A   A+++AG   +++DLIE NEAFA+QSLAV + L  + + +NVNGGAIALGHP+
Sbjct: 290 GPIEAIPKALKQAGLKKEDIDLIELNEAFASQSLAVIRTLDLNPDVINVNGGAIALGHPL 349

Query: 351 GASGARILVTLVHAMQKRDAKKGLATLCIGGGQGTAILLE 390
           G +GA++ V +++ +++++ K G+ T+C+G GQG A + E
Sbjct: 350 GCTGAKLTVQIMNELKRQNKKYGMVTMCVGTGQGAAGIFE 389


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: 427
Number of extensions: 21
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: 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.

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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