GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Sphingomonas koreensis DSMZ 15582

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate Ga0059261_2551 Ga0059261_2551 Acetate kinase

Query= curated2:Q1QPW6
         (404 letters)



>FitnessBrowser__Korea:Ga0059261_2551
          Length = 365

 Score =  212 bits (539), Expect = 2e-59
 Identities = 142/393 (36%), Positives = 201/393 (51%), Gaps = 45/393 (11%)

Query: 3   SILVVNAGSSSVKFQVFSAEGEGKLLRQIKGQVDGIGSRPRLRASGAD-NEPLADRAYPI 61
           +IL +NAGS+S+K  +   +   ++L   +   +  G R  +   G   N  L + A  I
Sbjct: 4   AILTLNAGSTSLKASLRLLDAPTQVLWSSQATAERDGWRLDIVGPGETVNGGLEEVASRI 63

Query: 62  --ESVSDVPAAMGVAGGWLRDELRISPMAVGHRVVHGGPDYDRPVLIDHGVVARLERFVA 119
             ++  D+P+              +    V HR+VHGG D+  P ++D   + RL     
Sbjct: 64  LDQAAIDIPS--------------VEIAVVAHRIVHGGADFSEPTILDDVKIGRLRDLTR 109

Query: 120 LAPLHQPNNLDPIRSLLANFPALPQVACFDTAFHRTHDAVADYYAIPYQFYVE--GVRRY 177
            AP HQ   LD  +SL    P   Q+ CFDTAFH +   +   Y +P    +   G RRY
Sbjct: 110 YAPQHQGPALDIAQSLGIAQPDTLQIGCFDTAFHASISPLN--YELPLYEGLRKLGYRRY 167

Query: 178 GFHGLSYEYVAKTLPHVAPEIAKGRVIVAHLGSGASMCALKGGRSIESTMGFTALDGLPM 237
           GFHGLSY+ +A  L    PE+   RV+VAHLG G+S+CAL  GRS+ +TMG TALDG+PM
Sbjct: 168 GFHGLSYQSIAARLSAERPELE--RVVVAHLGGGSSLCALHHGRSVATTMGMTALDGVPM 225

Query: 238 GTRPGQIDPGVVLYLVSEKGMSPAKAQDFLYRDCGLKGLSGVSNDMRELEASEDPKAKLA 297
            TR G IDPGV+L LV + G+     +D LY   GL  LSG   D+R + A++   A  A
Sbjct: 226 KTRSGAIDPGVILDLVKDAGVE--VVEDLLYHKSGLASLSGTDGDLRTIRATDTEAAAFA 283

Query: 298 VDYFVYRVGLNAGMLAAALQGLDAFVFTAGIGENSMRIRARIADQLAWLGVTLDPTQNSR 357
           VDY+V R+   A  L  +L G+ A VFT G+G N + I   +A +L  L           
Sbjct: 284 VDYWVLRIAEAAAALGVSLGGMQALVFTGGVGSNDIAIGDAVAARLHHL----------- 332

Query: 358 HARLISGSDSRIPVYVIPTDEELMIAQHTLSLL 390
                        +  + TDEEL++AQ   +L+
Sbjct: 333 ---------PSFELIRLRTDEELVLAQAAQTLI 356


Lambda     K      H
   0.320    0.137    0.403 

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: 374
Number of extensions: 21
Number of successful extensions: 5
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: 404
Length of database: 365
Length adjustment: 30
Effective length of query: 374
Effective length of database: 335
Effective search space:   125290
Effective search space used:   125290
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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