GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdaD in Burkholderia phytofirmans PsJN

Align 2-keto-3-deoxyxylonate dehydratase (EC 4.2.1.141) (characterized)
to candidate BPHYT_RS28765 BPHYT_RS28765 fumarylacetoacetate hydrolase

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



>FitnessBrowser__BFirm:BPHYT_RS28765
          Length = 394

 Score =  447 bits (1150), Expect = e-130
 Identities = 225/390 (57%), Positives = 285/390 (73%), Gaps = 5/390 (1%)

Query: 6   SLQAHLPEDHAQATLIGRIWQP---GVGPVLVRIDADGAYDLTLIAATSSELLELDNPAA 62
           S  ++LP+D   A L+GR+W+    G GP +V +     +D++ +A T S+L +  +   
Sbjct: 3   SYSSYLPDDLDGALLVGRVWRQTNSGAGPCVVAVRGGEVFDISRLAPTVSDLFDRQDLVE 62

Query: 63  AVRSATNMTRIATLQELLDNADAAGRDTSRPWLLAPIDLQAVKASGVTFVASMLERVIEE 122
            VR A   + +  + +L++   AA R   +P+LLAP DLQA+KA GVTF  S+LERVIEE
Sbjct: 63  LVRQAAGES-LGYVDDLIETTVAAQRKEDQPYLLAPCDLQAIKACGVTFAVSLLERVIEE 121

Query: 123 QARGDAGKAESVRKAITAVIGDNLSSVVPGSPEAARLKEVLLDQGVWSQYLEVGIGPDAE 182
           QA GD  KAE VR AIT +IG +LS + PGS  A +LKE L  +G WSQY+EVGIGPDAE
Sbjct: 122 QAGGDPAKAEEVRAAITRLIGTDLSKIKPGSEAAVKLKEELQRRGAWSQYMEVGIGPDAE 181

Query: 183 IFTKAQPMSSVGLGDEVGIHPKSAWNNPEPEIVLAINSRGKVVGATLGNDVNLRDFEGRS 242
           +F+KAQPMSSVGLG ++G+ P S WNNPEPEIVLA+NS+G+VVGATLGNDVNLRD EGRS
Sbjct: 182 VFSKAQPMSSVGLGADIGLLPASKWNNPEPEIVLAVNSKGEVVGATLGNDVNLRDIEGRS 241

Query: 243 ALLLGKAKDNNASCAVGPFIRLFDANFSIDDVRRAELTMRVDGT-EGFTLKGSSSMSMIS 301
           ALLLGK KDNN SCA+GPFIRLFD  F++D +R   +++RV+GT +GF L+G S M  IS
Sbjct: 242 ALLLGKCKDNNGSCAIGPFIRLFDGRFTLDTIRATSVSLRVEGTDDGFVLEGVSHMQEIS 301

Query: 302 RDPLQLVEHAIGPNHQYPDGLVLFLGTMFAPTQDRFGPGQGFTHQVADIVTISTPKLGAL 361
           RDP+ LV    G +HQYPDG +LFLGTMF+P +DR  PG GFTH + D VTIS P LGAL
Sbjct: 302 RDPIDLVSQTWGKHHQYPDGFMLFLGTMFSPIKDRDAPGGGFTHHLGDRVTISAPPLGAL 361

Query: 362 VNTVNFSDQTAPWTFGLTALFKNLADRKLI 391
           VNTV  S + APWTFG+ AL+ NLA+R L+
Sbjct: 362 VNTVRLSTEIAPWTFGVRALYANLAERSLL 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: 461
Number of extensions: 17
Number of successful extensions: 4
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: 394
Length adjustment: 31
Effective length of query: 360
Effective length of database: 363
Effective search space:   130680
Effective search space used:   130680
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