GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolJ in Collinsella tanakaei YIT 12063

Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate WP_009140764.1 HMPREF9452_RS03670 class II fructose-bisphosphate aldolase

Query= SwissProt::P42420
         (290 letters)



>NCBI__GCF_000225705.1:WP_009140764.1
          Length = 282

 Score =  204 bits (519), Expect = 2e-57
 Identities = 111/283 (39%), Positives = 164/283 (57%), Gaps = 5/283 (1%)

Query: 4   VSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGFKTI 63
           V+ KE+L DA++  YA+G FN+  L++  A+L AA++ +SPVI   +   +   G     
Sbjct: 3   VTTKEMLLDAQKNHYAVGAFNVENLEFVMAVLAAAEETKSPVIMQTTSGTIKKTG-LDYF 61

Query: 64  AAMVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGSHQPIDENIAMTKEV 123
             MV A  E    +VPV LHLDHG   +RC +A+  G++SVMIDGSH+  ++NIA+TK V
Sbjct: 62  YGMVKAAAE--RASVPVALHLDHGDGYDRCMKALRTGYTSVMIDGSHETFEDNIALTKLV 119

Query: 124 TDYAAKHGVSVEAEVGTVGGMEDGLV--GGVRYADITECERIVKETNIDALAAALGSVHG 181
            D  A  G+ VEAE+G VGG ED +   G   Y D  E +  V+ T   +LA  +G+ HG
Sbjct: 120 ADAGAAMGIPVEAELGKVGGKEDDVEVEGESPYTDPVEAKEFVERTGCTSLAIGVGTAHG 179

Query: 182 KYQGEPNLGFKEMEAISRMTDIPLVLHGASGIPQDQIKKAITLGHAKININTECMVAWTD 241
            Y  EP++    ++AI    D+PLVLHG SG+P +Q+ +A+  G  K+N  TE   A+T 
Sbjct: 180 VYTEEPHIDQDVVKAIRAAVDVPLVLHGTSGVPDEQVAEAVKNGICKVNYATELRQAYTK 239

Query: 242 ETRRMFQENSDLYEPRGYLTPGIEAVEETVRSKMREFGSAGKA 284
                  EN + ++P+     G E + + V+ +M   GS G+A
Sbjct: 240 GYMAYMAENPNNFDPKNPGKAGAEEITKIVKIRMENLGSVGRA 282


Lambda     K      H
   0.316    0.132    0.372 

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: 226
Number of extensions: 5
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: 290
Length of database: 282
Length adjustment: 26
Effective length of query: 264
Effective length of database: 256
Effective search space:    67584
Effective search space used:    67584
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: 47 (22.7 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