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

GapMind for catabolism of small carbon sources

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

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate H281DRAFT_03563 H281DRAFT_03563 FAD/FMN-containing dehydrogenase

Query= reanno::Putida:PP_4493
         (1006 letters)



>FitnessBrowser__Burk376:H281DRAFT_03563
          Length = 1006

 Score =  327 bits (838), Expect = 3e-93
 Identities = 282/1018 (27%), Positives = 445/1018 (43%), Gaps = 114/1018 (11%)

Query: 21  LRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVARVATLMGEPRFQQVKL 80
           LR S  RG +  D A+R   ATD SIYQ +P   V P D DD+ R+A  +   R ++V L
Sbjct: 30  LRKS-LRGDVLFDAASRGRYATDASIYQIMPVGVVVPRDQDDL-RIA--LDIARSEKVPL 85

Query: 81  TPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAGTVKDQLNAALKPHGLF 140
             RG GT   GQ++ + +V+D S+ +NNI++ N+E R V V+ G V D LNA LKPHGL+
Sbjct: 86  LARGAGTSQCGQTVGEALVIDTSKWLNNIVDFNLEARTVTVEPGVVLDHLNAWLKPHGLW 145

Query: 141 FAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLLGGERLHSLPIDDAALE 200
           F  ++ST+ + T+GGM   ++ G  S  YG    +V  + ++L  G       + DA   
Sbjct: 146 FPVDVSTAAQCTIGGMAGNNSCGSRSIEYGNMVHNVEAIDAILADGTEARFASLRDA--- 202

Query: 201 QACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTGYDL-------AHLRDEQGRF 253
                  R+ +++   R+I + + + I    PK+ R + GY++            + G  
Sbjct: 203 ---PQGARLQQIFEGVRQIAQRERDEIVARVPKVLRRVAGYNIDLFDCQNPRAYTDDGVA 259

Query: 254 NLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDANALMAHKPLSIET 313
           NL  +L G+EG+L +  +  L + P+P +  L  V + +F  ++     ++  KP+++E 
Sbjct: 260 NLAHLLVGSEGTLAFSRQLTLKLAPLPAHKTLGVVNFPTFWQSMDLTQHIVKLKPVAVEL 319

Query: 314 VDSKVLMLAMKDIVWHSVAE-YFPADPERPTLGINLVEFCGDEPAEVNAKVQAFIQHLQS 372
           VD  ++ LAM +  +  V E     +P+     + LVEF G E  +   +    +  L +
Sbjct: 320 VDRTMIDLAMSNPAFRPVVEKALVGEPQ----AVLLVEFAG-ESRDAQLESLRQLSELMA 374

Query: 373 DTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPPEQLADYIA 432
           D  +      + + A A   ++ +RK  + ++ +++G+ +P  F+ED AVP E LA+Y +
Sbjct: 375 DLGLPGSVVEMPD-ANAQKALWEVRKAGLNIMMSMKGDGKPVSFIEDCAVPLEHLAEYTS 433

Query: 433 DFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALTKRYGGLLW 492
               +   +G     + H   G LHVRP LDM+    A  ++ I++  AAL + Y G   
Sbjct: 434 QLTEVFHRHGTEGTWYAHASVGTLHVRPILDMRRD-GAVKMRAIAEQAAALVREYKGAYS 492

Query: 493 GEHGKGL-RSEYVPEYFG-ELYPALQRLKGAFDPHNQLNPGKICTP--LGSAEGLTPVDG 548
           GEHG GL R E+V   +G +L  A   +K  FDP N+ NP K+  P  +          G
Sbjct: 493 GEHGDGLCRGEWVAWQYGPKLNQAFSEIKALFDPDNRFNPDKMVRPPKMDDPRYFRFAPG 552

Query: 549 VTLRGDLDRTIDERVWQ---------------------DFPSAVH-CNGNGACYNYDPND 586
              R  ++  +D   W                          AV  CN NG C  +D   
Sbjct: 553 YQER-PIEPALDWSAWNVERDPLTGRETAPGSGNDLAGGLAKAVEMCNNNGHCRKFDAG- 610

Query: 587 AMCPSWKATRERQHSPKGRASLMREWLRLQGEANIDVLAAARNKVSWLKGLPARLRNNRA 646
            MCPS++ T++ QH  +GRA+ +R  L + G+     LA                     
Sbjct: 611 TMCPSYRVTKDEQHVTRGRANTLR--LAISGQLGEAGLA--------------------- 647

Query: 647 RNQGQEDFSHEVYDAMAGCLACKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIG 706
                   S EV D +  C++CK C   CP  V++  F+         R+   LRD L+ 
Sbjct: 648 --------SDEVKDTLDLCVSCKGCKRDCPTGVDMAKFKIEARAARVKRHGLTLRDKLVA 699

Query: 707 SLEFTIPYLAHAPGLYNAVMGSKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATV 766
            +       +  PGL         VS L    VG      + RF      +      A  
Sbjct: 700 FMPRYAAAASRMPGLIAVADNVPLVSSLFKRAVGFASERSLPRFRKSFLSSASPTVNAHG 759

Query: 767 PALRELTPAQRERSIVLVQDAFTRYFETPLLSAFIDLAHRLGHRVFLAPYSAN-----GK 821
             L+E         ++L  D F    E     A   +    G+ V             G+
Sbjct: 760 ATLKE---------VLLFVDTFNNSMEPENARAAQKVLEAAGYTVHFNMREGERPVCCGR 810

Query: 822 PLHVQGFLGAFAKAAIRNATQLKALADCGVPLVGLDPAMTLVYRQEYQKVPGLEGCPKVL 881
                G +      A R         + GVP+VGL+P+  L  R E+    G     + L
Sbjct: 811 TFLAAGLVDEAKHEARRMLDLFNPFVERGVPIVGLEPSCLLSLRDEFLHY-GFGDEAQQL 869

Query: 882 LPQEWLMD---VLPEQA--------PAAPGSFRLMAHCTEKTNVPASTRQWEQVFARLGL 930
             Q +L +   V  E+A        P       +  HC +K    A T     +     L
Sbjct: 870 AKQAFLFEEFLVREEKAGRLELALKPLDTPQALVHGHCHQKA-FDAFTPVQTVLKWIPEL 928

Query: 931 KLVTEATGCCGMSGTYGHEARNQETSRTIFEQSW---ATKLDKDGEPLATGYSCRSQV 985
           K+ T  + CCGM+G++G+EA +  TS+ + E S      K+D +   +A G SCR Q+
Sbjct: 929 KVSTVESSCCGMAGSFGYEAEHYATSQAMAELSLLPAVRKIDGNTVMVADGTSCRHQI 986


Lambda     K      H
   0.320    0.135    0.409 

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: 2306
Number of extensions: 105
Number of successful extensions: 13
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 2
Length of query: 1006
Length of database: 1006
Length adjustment: 45
Effective length of query: 961
Effective length of database: 961
Effective search space:   923521
Effective search space used:   923521
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 (21.8 bits)
S2: 57 (26.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources