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_05881 H281DRAFT_05881 D-amino-acid dehydrogenase

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



>FitnessBrowser__Burk376:H281DRAFT_05881
          Length = 414

 Score =  421 bits (1081), Expect = e-122
 Identities = 222/415 (53%), Positives = 266/415 (64%), Gaps = 5/415 (1%)

Query: 1   MHCQTLVLGAGIVGVSTALHLQARGRQVILIDRDEPGSGTSHGNAGLIERSSVIPYAFPR 60
           M    +VLG GIVGVS ALHLQ RGR+V L+DR  PG  TS GNAGLIER++V+PY FPR
Sbjct: 1   MDFDVIVLGGGIVGVSCALHLQDRGRRVALVDRRAPGEETSFGNAGLIERAAVVPYGFPR 60

Query: 61  QLSALLRYGLNRQPDVRYSLAHLPKAAPWLWRYWRQSAPGRLAGAAADMLPLVQRCVDEH 120
            L  LLR+  NR  D+ +    +P  A WL R+W +S+  RL  AA DMLPL++R V EH
Sbjct: 61  DLRTLLRFAKNRSTDLYWDYRAVPHFATWLARFWWESSAERLMAAARDMLPLIERSVTEH 120

Query: 121 DALIAAAGLEGLVQAKGWIEVFRDPA-LFEQAKTDAKGLSRYGLRFEILECGQLQAREHQ 179
           + LI  A L+ LV+A GWI+ +R PA L  +A         YGLR  +L+ G L ARE  
Sbjct: 121 ERLIKRAELQHLVRATGWIDAYRTPARLAREAAAAEATAGSYGLRVSVLDGGTLAAREPG 180

Query: 180 LDATVVGGIHWLDPKTVNNPGALTRGYAALFLQRGGQFVHGDARSLRQANGQWRVESRRG 239
                 G +HW DP +V NPG LT+GYA LF   GG  + GDA +L    G W V++  G
Sbjct: 181 AVGGFCGALHWQDPMSVVNPGELTKGYARLFEASGGVVLTGDAATLSGRAGAWTVQTTSG 240

Query: 240 PITADEVVACLGPQSADLFSGLGYQIPLAIKRGYHMHY-STRDGAQLEHSICDTQGGYVL 298
            I+A E V  LGP S  +F+ LGY+IPL +KRGYHMHY  TR    L     D + GYV+
Sbjct: 241 RISAKEAVVALGPWSDCVFAPLGYRIPLRVKRGYHMHYRPTR--PMLSMPFVDAEQGYVV 298

Query: 299 APMARGVRLTTGIEFDAASAPGNQIQLGRCEALARKLFPALGDRLDDTPWLGRRPCLPDM 358
           APM   +RLTTG+E     A    IQLGR E  AR  F  LG+RLDD+PWLG RPC PDM
Sbjct: 299 APMEGRLRLTTGVEIARRDAEPTGIQLGRAERFARPSF-GLGERLDDSPWLGLRPCTPDM 357

Query: 359 RPVIGPAPRHPGLWFNFGHAHHGLTLGPVCGRLLAELLTGEPPFTDPAPYSATRF 413
           RPVIG APRH GLWF FGH HHGLTLGP  GRLLAE++TG P F DP P+   RF
Sbjct: 358 RPVIGRAPRHTGLWFAFGHNHHGLTLGPATGRLLAEMMTGAPTFADPHPFRVERF 412


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: 550
Number of extensions: 19
Number of successful extensions: 5
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: 414
Length adjustment: 31
Effective length of query: 383
Effective length of database: 383
Effective search space:   146689
Effective search space used:   146689
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