GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Pseudovibrio axinellae Ad2

Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate WP_068010615.1 PsAD2_RS21780 ROK family protein

Query= SwissProt::P23917
         (302 letters)



>NCBI__GCF_001623255.1:WP_068010615.1
          Length = 311

 Score =  180 bits (457), Expect = 3e-50
 Identities = 104/294 (35%), Positives = 156/294 (53%), Gaps = 3/294 (1%)

Query: 4   GIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGT-VGM 62
           GIDLGGTK E  A  +A   +   R+ TP++ Y   ++ +  ++   E+ +G +   +G+
Sbjct: 6   GIDLGGTKIEATAFDEAWAVVESKRIATPKETYEGLVDALCEMIHWLEEVSGNKDLPIGV 65

Query: 63  GIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAAGA 122
           GIPG  S  TG    AN    +G+    D+ ++L R V   ND NC A+SEAV GA    
Sbjct: 66  GIPGFYSKRTGKFLTANLP-ASGRTLHDDIISKLGRAVTFENDCNCFALSEAVLGAGRSY 124

Query: 123 QTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCGKQG 182
            TVF +I+GTG G G   NG    G NG AGE+GH  +P+    +L   E + C CG+ G
Sbjct: 125 DTVFGLILGTGVGGGCCSNGHTVSGLNGAAGEYGHLGIPYAAMTKLGL-EPLKCGCGRTG 183

Query: 183 CIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHVVNI 242
           C ET+++G G +     ++G A+    I +     D   +  +R +    A+ +A +   
Sbjct: 184 CFETYLAGPGISRLANHVTGKAVDAQTITKAAAAGDVPMQEVMRLWSQLAAELVAALQCS 243

Query: 243 LDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAA 296
           LDPD IVLGGG+S +  + +T+ Q +   +        +  A+ GDSSG RGAA
Sbjct: 244 LDPDCIVLGGGLSKIPNIERTIAQALPGKLLNHTEPPMICVAQFGDSSGTRGAA 297


Lambda     K      H
   0.318    0.137    0.418 

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: 315
Number of extensions: 17
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: 302
Length of database: 311
Length adjustment: 27
Effective length of query: 275
Effective length of database: 284
Effective search space:    78100
Effective search space used:    78100
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: 48 (23.1 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