GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ketodeoxyribonate-cleavage in Acidovorax sp. GW101-3H11

Align 2-deoxy-3-keto-D-ribonate cleavage enzyme (characterized)
to candidate Ac3H11_1929 FIG00537796: hypothetical protein

Query= reanno::Burk376:H281DRAFT_00641
         (312 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1929
          Length = 303

 Score =  135 bits (341), Expect = 9e-37
 Identities = 99/309 (32%), Positives = 158/309 (51%), Gaps = 28/309 (9%)

Query: 4   TSRKVIISCAITGATHVPSMSEFLPITPEQIRDQAIEAAQAGAAIIHLHARDPVDGR--- 60
           TS K II+CAITG    P     +P+TPEQ+  +A  A  AGAA++H+H R+   G+   
Sbjct: 7   TSNKAIITCAITGVLTDPGQHH-VPVTPEQLAKEARGACDAGAAVVHVHFRNQEPGKGHL 65

Query: 61  PTPSPEIFKAFVPAIAEATDAVINITTGGSTRMTLEERLAYPRLARPEMCSLNMGSMNFS 120
           P+  P++ +  V A+ EA   +I   T G      +  L   R  RPEM + N GS+N+ 
Sbjct: 66  PSWDPQVARDCVQAMREACPGLIINQTTGVVGPHYQGPLDCLRATRPEMAACNAGSLNY- 124

Query: 121 IHPVAAKI-SSWRYGWEKDYIEGMEDMIFRNTFRDIRNILLELGESGTRFEFECYDVGHL 179
                 K+ S+  + W          M+F N    +++ +  + E+GT  EFEC+DVG +
Sbjct: 125 -----LKVRSNGTWAWPP--------MLFDNQPAKVKDFIDVMLETGTLPEFECFDVGIV 171

Query: 180 YNLAHFVDQGLVK---PPFFIQSVFGILGGLGADPENMLLMRSTADRLFGRENYHFSVLG 236
             +  +V  G+     P +    V G+  G+ ADP+ + ++     ++ G   +  +V+G
Sbjct: 172 RCVEMYVQTGMYTERLPEY--NFVMGVESGMPADPDLLPILLKL--KIKGAP-WQATVIG 226

Query: 237 AGRHQMPLVTMSAIMGGNVRVGLEDSVYLAKGVKAETNAQQVRKIRRILEELSLEIATPA 296
                 P+    A +GG++R GLED+ YL  G KA++N   + K+         E+A+P 
Sbjct: 227 RSEI-WPVHQRVAELGGHLRTGLEDTFYLPDGTKADSNGPLIEKLAEYARNAGREVASPQ 285

Query: 297 DARKMLGLK 305
           +AR MLGLK
Sbjct: 286 EARGMLGLK 294


Lambda     K      H
   0.321    0.137    0.400 

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: 240
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: 312
Length of database: 303
Length adjustment: 27
Effective length of query: 285
Effective length of database: 276
Effective search space:    78660
Effective search space used:    78660
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 (21.9 bits)
S2: 48 (23.1 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