GapMind for catabolism of small carbon sources

 

Alignments for a candidate for odc in Burkholderia phytofirmans PsJN

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate BPHYT_RS00645 BPHYT_RS00645 diaminopimelate decarboxylase

Query= BRENDA::C9W982
         (420 letters)



>FitnessBrowser__BFirm:BPHYT_RS00645
          Length = 402

 Score = 79.0 bits (193), Expect = 2e-19
 Identities = 106/352 (30%), Positives = 152/352 (43%), Gaps = 55/352 (15%)

Query: 29  YAVKCNPDPVMLRVLANLGCGFDCASAKEMATVLDMGVEAESIVFAHPCKRPLDLEFAIE 88
           Y++K NP P ++  LA    GFD ASA+EMA  LD G   +SI FA P K   DL  A+ 
Sbjct: 58  YSIKANPMPAVIHYLAQRVDGFDVASAQEMALALDAGATPDSIGFAGPGKSHDDLRRAVA 117

Query: 89  TNVTRMTFDCVDELEKVAA----ECPHAELVLRIRADDPSAVVQFGHK----------YG 134
           + V  +  +   +L  V A          +V+RI  D      Q GH           +G
Sbjct: 118 SGV-NVHVESDTQLRLVTALGWELGVQPNVVIRINPD-----FQVGHSGMRMGGSAAPFG 171

Query: 135 ADPQTEAPMLLAAAKQLEMNVVGVSFHVGSGSQSCDAYPLAVEAARRVFD----QAADLG 190
            D   + P LL   +  E+ + G  FHV  GSQ   A  + +EA R+  D     A+DL 
Sbjct: 172 VDVD-QIPALLHELETREVALAG--FHVFWGSQCLHASTI-IEAQRQSVDLILRLASDLP 227

Query: 191 YEMQLLDLGGGFWGRFDATGHVPLED--VSEAINSALDRF-------FPVNSSGRKVEVI 241
             ++ ++LGGGF G     G  PL+   V EA++  L R         P+   GR   ++
Sbjct: 228 RPLRFVNLGGGF-GIPYFPGETPLDTKVVCEAMHDWLPRLCERLPGTTPILELGR--YLV 284

Query: 242 AEPGRYFAEACTTMYALVTTVKDRP-DGSRSYYITDGVYGSFNNLVYDHGSVTAKVLRGP 300
            E G Y           V  V DR     R++ ITDG  G  ++L    G+    + R  
Sbjct: 285 GEAGIY-----------VCRVIDRKVSRGRTFVITDG--GLHHHLAAS-GNFGQVLRRNF 330

Query: 301 GMPPVQPVETETRLPSTVFGPTCDGVDLIFKDVPMPLLRRGDWLQFPNFGAY 352
            +      +  +R    V G  C  +D +  DV +P    GD++     GAY
Sbjct: 331 PVVIGNRPDGISRERCYVVGCLCTPLDRLADDVELPEAHIGDFVVVKQSGAY 382


Lambda     K      H
   0.321    0.137    0.426 

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: 416
Number of extensions: 19
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: 420
Length of database: 402
Length adjustment: 31
Effective length of query: 389
Effective length of database: 371
Effective search space:   144319
Effective search space used:   144319
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