GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuA in Burkholderia phytofirmans PsJN

Align D-galactonate dehydratase family member PC1_0802; EC 4.2.1.-; D-mannonate dehydratase; EC 4.2.1.8 (uncharacterized)
to candidate BPHYT_RS23430 BPHYT_RS23430 bifunctional D-altronate/D-mannonate dehydratase

Query= curated2:C6D9S0
         (404 letters)



>FitnessBrowser__BFirm:BPHYT_RS23430
          Length = 402

 Score =  670 bits (1728), Expect = 0.0
 Identities = 315/404 (77%), Positives = 349/404 (86%), Gaps = 2/404 (0%)

Query: 1   MKIVSAEVFVTCPGRNFVTLKITTDSGLTGLGDATLNGRELPVASYLNDHVCPQLIGRDA 60
           MKIV A+V VTCPGRNFVTLKI TD G+ G+GDATLNGREL VASYL DHVCP LIGRD 
Sbjct: 1   MKIVRADVIVTCPGRNFVTLKIVTDEGVHGIGDATLNGRELAVASYLKDHVCPLLIGRDP 60

Query: 61  HQIEDIWQYFYKGAYWRRGPVTMSAISAVDMALWDIKAKAANMPLYQLLGGASRTGVMVY 120
             IED WQY YKGAYWRRGPVTM+AI+AVDMALWDI  K   MPLY+LLGGASR  VMVY
Sbjct: 61  GCIEDTWQYLYKGAYWRRGPVTMTAIAAVDMALWDILGKVTGMPLYKLLGGASRESVMVY 120

Query: 121 CHTTGHSIDEVLDDYAKHRDQGFKAIRVQCGVPGMETTYGMAKGKGLAYEPATKGSLPEE 180
            H TG  I E LD YA+H + G++AIR+QCGVP M + YG++KG G+ YEPATKG++ EE
Sbjct: 121 GHATGRDIPEALDRYAEHIEAGYQAIRIQCGVPNMRSVYGVSKGSGM-YEPATKGAV-EE 178

Query: 181 QLWSTEKYLDFTPKLFEAVRDKFGFNEHLLHDMHHRLTPIEAARFGKSVEDYRLFWMEDP 240
           Q WS+EKYLDF PKLFEAVRDKFGF+ HLLHD+HHRLTPIEAAR GKS+E YRLFWMEDP
Sbjct: 179 QSWSSEKYLDFVPKLFEAVRDKFGFDTHLLHDVHHRLTPIEAARLGKSIEPYRLFWMEDP 238

Query: 241 TPAENQACFRLIRQHTVTPIAVGEVFNSIWDCKQLIEEQLIDYIRTTITHAGGITGMRRI 300
           TPAENQA FRLIR+HTVTPIAVGEVFNSIWDCKQLIEEQLIDYIR T+THAGGIT +RRI
Sbjct: 239 TPAENQAGFRLIREHTVTPIAVGEVFNSIWDCKQLIEEQLIDYIRATLTHAGGITHLRRI 298

Query: 301 ADFASLYQVRTGSHGPSDLSPICMAAALHFDLWVPNFGVQEYMGYSEQMLEVFPHSWTFD 360
           ADFASLYQVRTG HGPSDLSP+CM AALHFDLWVPNFGVQEYMG+ ++ L+VFPH+W F+
Sbjct: 299 ADFASLYQVRTGCHGPSDLSPVCMGAALHFDLWVPNFGVQEYMGFPQEALDVFPHAWRFE 358

Query: 361 NGYMHPGEKPGLGIEFDEKLAAKYPYDPAYLPVARLEDGTLWNW 404
            G MHPGE PG G++ DE  AA+YPYDPAYLPVARLEDGTLWNW
Sbjct: 359 RGTMHPGEAPGHGVDIDEAAAARYPYDPAYLPVARLEDGTLWNW 402


Lambda     K      H
   0.321    0.138    0.442 

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: 708
Number of extensions: 33
Number of successful extensions: 3
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: 404
Length of database: 402
Length adjustment: 31
Effective length of query: 373
Effective length of database: 371
Effective search space:   138383
Effective search space used:   138383
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: 50 (23.9 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