GapMind for catabolism of small carbon sources

 

Aligments for a candidate for put1 in Burkholderia phytofirmans PsJN

Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate BPHYT_RS29290 BPHYT_RS29290 D-amino acid oxidase

Query= BRENDA::Q5JFG7
         (386 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS29290 BPHYT_RS29290 D-amino acid
           oxidase
          Length = 441

 Score =  144 bits (362), Expect = 6e-39
 Identities = 115/423 (27%), Positives = 181/423 (42%), Gaps = 61/423 (14%)

Query: 6   LPEKSEITIIGGGIVGVTIAHELAKRGEEVTVIEKRFIGSGSTFRCGTGIRQQFNDEANV 65
           LP  +++ +IGGGI+GV  A+ +A+RG  V ++EK  IG+  + R     RQQ  DE  +
Sbjct: 14  LPAAADVVVIGGGIIGVFAAYYMAQRGVSVALVEKGRIGAEQSSRNWGWCRQQNRDEREL 73

Query: 66  QVMKRSVELWKKYSEEYG--FPFQQTGYLFLLYDDEEVETFKRNIAIQNKFGVPTRLITP 123
            +  +S++LW++++ E G    F + G L+L  DD E+  +          GV T L+  
Sbjct: 74  PIASKSLDLWERFAVESGEDTGFHRCGLLYLSNDDAELARWASWGDFAKTAGVTTYLLDS 133

Query: 124 EEAKEIVPLLDISEVVAASW-----NPTDGKASPFHSTAKFALHAEEFGAKLVEYTEVKD 178
           ++A E        +    +W     +P+DG A P  +    A    + G  + +    + 
Sbjct: 134 KQAAE------RGKATGRAWKGGVFSPSDGTADPAKAAPAVATALMKLGGSVTQQCAARG 187

Query: 179 FIIENGEIKGLKTSRGTIKTGIVVNATNAWAKLINAMAGIR-----------TKIPIEPY 227
             +E G + G+ T  G IKT  VV A  AWA       GIR           +  P+E  
Sbjct: 188 IELEGGRVCGVVTEAGVIKTRTVVLAGGAWASAFCRQLGIRFPQASIRQSILSVSPVETP 247

Query: 228 KHQAVITQPIK-----------------KGSVKPMVISF--RYGHAYLTQTSH---GGII 265
              A+ T  +                  +  V P  + F  ++   +  +  +   GG+ 
Sbjct: 248 LPDALFTSGVSITRRTDGRYALAISGRARVDVTPQFLRFAPQFVPMFAKRWRNLLPGGLE 307

Query: 266 GGVGYEE--------GPT-------YDLNPTYEFLREVSYYFTKIIPALRELLILRTWAG 310
           G  G  E         PT        D  P    +RE      +++P L +  I   WAG
Sbjct: 308 GVRGGHETLKRWQLDAPTPMERVRILDPKPDMPTVRETHRRAIELLPELGKAKITHAWAG 367

Query: 311 YYAKTPDSNPAIGKIEELSDYYIAAGFSGHGFMMAPAVAEMVADLITKGKTDLPAWWYDP 370
           +   TPD  P IG++  +    +AAGFSGHGF + P    ++ADL T     +    Y P
Sbjct: 368 FVDSTPDGVPGIGEVPGVPGLILAAGFSGHGFGIGPGAGHLIADLATGAAPIVDPIPYRP 427

Query: 371 YRF 373
            RF
Sbjct: 428 ARF 430


Lambda     K      H
   0.318    0.137    0.406 

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: 395
Number of extensions: 19
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 386
Length of database: 441
Length adjustment: 31
Effective length of query: 355
Effective length of database: 410
Effective search space:   145550
Effective search space used:   145550
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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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