GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdaD in Herbaspirillum seropedicae SmR1

Align 2-keto-3-deoxyxylonate dehydratase (EC 4.2.1.141) (characterized)
to candidate HSERO_RS19360 HSERO_RS19360 fumarylacetoacetate hydrolase

Query= reanno::HerbieS:HSERO_RS19360
         (391 letters)



>FitnessBrowser__HerbieS:HSERO_RS19360
          Length = 391

 Score =  769 bits (1985), Expect = 0.0
 Identities = 391/391 (100%), Positives = 391/391 (100%)

Query: 1   MAHTFSLQAHLPEDHAQATLIGRIWQPGVGPVLVRIDADGAYDLTLIAATSSELLELDNP 60
           MAHTFSLQAHLPEDHAQATLIGRIWQPGVGPVLVRIDADGAYDLTLIAATSSELLELDNP
Sbjct: 1   MAHTFSLQAHLPEDHAQATLIGRIWQPGVGPVLVRIDADGAYDLTLIAATSSELLELDNP 60

Query: 61  AAAVRSATNMTRIATLQELLDNADAAGRDTSRPWLLAPIDLQAVKASGVTFVASMLERVI 120
           AAAVRSATNMTRIATLQELLDNADAAGRDTSRPWLLAPIDLQAVKASGVTFVASMLERVI
Sbjct: 61  AAAVRSATNMTRIATLQELLDNADAAGRDTSRPWLLAPIDLQAVKASGVTFVASMLERVI 120

Query: 121 EEQARGDAGKAESVRKAITAVIGDNLSSVVPGSPEAARLKEVLLDQGVWSQYLEVGIGPD 180
           EEQARGDAGKAESVRKAITAVIGDNLSSVVPGSPEAARLKEVLLDQGVWSQYLEVGIGPD
Sbjct: 121 EEQARGDAGKAESVRKAITAVIGDNLSSVVPGSPEAARLKEVLLDQGVWSQYLEVGIGPD 180

Query: 181 AEIFTKAQPMSSVGLGDEVGIHPKSAWNNPEPEIVLAINSRGKVVGATLGNDVNLRDFEG 240
           AEIFTKAQPMSSVGLGDEVGIHPKSAWNNPEPEIVLAINSRGKVVGATLGNDVNLRDFEG
Sbjct: 181 AEIFTKAQPMSSVGLGDEVGIHPKSAWNNPEPEIVLAINSRGKVVGATLGNDVNLRDFEG 240

Query: 241 RSALLLGKAKDNNASCAVGPFIRLFDANFSIDDVRRAELTMRVDGTEGFTLKGSSSMSMI 300
           RSALLLGKAKDNNASCAVGPFIRLFDANFSIDDVRRAELTMRVDGTEGFTLKGSSSMSMI
Sbjct: 241 RSALLLGKAKDNNASCAVGPFIRLFDANFSIDDVRRAELTMRVDGTEGFTLKGSSSMSMI 300

Query: 301 SRDPLQLVEHAIGPNHQYPDGLVLFLGTMFAPTQDRFGPGQGFTHQVADIVTISTPKLGA 360
           SRDPLQLVEHAIGPNHQYPDGLVLFLGTMFAPTQDRFGPGQGFTHQVADIVTISTPKLGA
Sbjct: 301 SRDPLQLVEHAIGPNHQYPDGLVLFLGTMFAPTQDRFGPGQGFTHQVADIVTISTPKLGA 360

Query: 361 LVNTVNFSDQTAPWTFGLTALFKNLADRKLI 391
           LVNTVNFSDQTAPWTFGLTALFKNLADRKLI
Sbjct: 361 LVNTVNFSDQTAPWTFGLTALFKNLADRKLI 391


Lambda     K      H
   0.317    0.134    0.387 

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: 647
Number of extensions: 13
Number of successful extensions: 1
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: 391
Length of database: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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