GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaD in Paraburkholderia bryophila 376MFSha3.1

Align D-lysine oxidase (EC 1.4.3.3) (characterized)
to candidate H281DRAFT_03160 H281DRAFT_03160 D-amino-acid dehydrogenase

Query= metacyc::G1G01-3833-MONOMER
         (414 letters)



>FitnessBrowser__Burk376:H281DRAFT_03160
          Length = 413

 Score =  415 bits (1066), Expect = e-120
 Identities = 216/410 (52%), Positives = 261/410 (63%), Gaps = 5/410 (1%)

Query: 5   TLVLGAGIVGVSTALHLQARGRQVILIDRDEPGSGTSHGNAGLIERSSVIPYAFPRQLSA 64
           T+VLGAGIVGV  A+HLQ RGRQV L+DR  PG+ TS GNAGLI+R  V PYAFPR L A
Sbjct: 8   TVVLGAGIVGVCVAVHLQQRGRQVALVDRKLPGNETSFGNAGLIQREGVYPYAFPRGLGA 67

Query: 65  LLRYGLNRQPDVRYSLAHLPKAAPWLWRYWRQSAPGRLAGAAADMLPLVQRCVDEHDALI 124
           LLRY  N+  DVRY    L  AAP+LWRYWR S P + A  A     L++ C+ EH  L 
Sbjct: 68  LLRYARNQSLDVRYHGDALFHAAPFLWRYWRNSEPAKHAAIAKSYSTLIEHCISEHRELA 127

Query: 125 AAAGLEGLVQAKGWIEVFRDPALFE-QAKTDAKGLSRYGLRFEILECGQLQAREHQLDAT 183
           A AG   L++  GWI+VFR  A  + + +   +    YG+ FE L+  +LQ  E  LD  
Sbjct: 128 ANAGASALLRPTGWIKVFRSNAAQDAEIRLAEQWRREYGVEFETLDAARLQQAEPDLDKA 187

Query: 184 VVGGIHWLDPKTVNNPGALTRGYAALFLQRGGQFVHGDARSLRQANGQWRVESRRGPITA 243
           + GG+ +    +V++P AL   YA  F   GG+   GDA +LR  NG W V +  G I A
Sbjct: 188 LQGGLRYTQADSVSDPNALVTAYAKYFETLGGRIFTGDANTLR--NG-WEVTTDAGTIAA 244

Query: 244 DEVVACLGPQSADLFSGLGYQIPLAIKRGYHMHYSTRDGAQLEHSICDTQGGYVLAPMAR 303
             VV  LGP S  L S LGY +PL +KRGYHMHYS R GA+L H + D + GY+LAPMAR
Sbjct: 245 SSVVVALGPWSDVLTSRLGYSLPLGVKRGYHMHYSPRAGARLNHPVLDVENGYLLAPMAR 304

Query: 304 GVRLTTGIEFDAASAPGNQIQLGRCEALARKLFPALGDRLDDTPWLGRRPCLPDMRPVIG 363
           G+RLTTG E     AP    QL   E +AR LFP L  R+DD PW+G RPC PDM PVIG
Sbjct: 305 GIRLTTGAEIALRDAPKTPTQLAAVEPIARTLFP-LDQRVDDQPWMGARPCTPDMMPVIG 363

Query: 364 PAPRHPGLWFNFGHAHHGLTLGPVCGRLLAELLTGEPPFTDPAPYSATRF 413
            A +H GLWF FGHAHHGLTLGPV GRL+AE++TGE    DP P+   RF
Sbjct: 364 RAGKHQGLWFAFGHAHHGLTLGPVTGRLIAEMMTGEQTLVDPRPFRVDRF 413


Lambda     K      H
   0.322    0.140    0.447 

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: 540
Number of extensions: 27
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: 414
Length of database: 413
Length adjustment: 31
Effective length of query: 383
Effective length of database: 382
Effective search space:   146306
Effective search space used:   146306
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