Alignments for a candidate for ydiJ in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for ydiJ in Burkholderia phytofirmans PsJN

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate BPHYT_RS34425 BPHYT_RS34425 lactate dehydrogenase

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



>FitnessBrowser__BFirm:BPHYT_RS34425
          Length = 1007

 Score =  330 bits (846), Expect = 3e-94
 Identities = 285/1019 (27%), Positives = 449/1019 (44%), Gaps = 115/1019 (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-LRGDVLFDAASRGRYATDASIYQITPIGVVVPRDQDDL-RIALEIA--RSEKVPL 85

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

Query: 141 FAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLLGGERLHSLPIDDAALE 200
           F  ++ST+ + T+GGM   ++ G  S  YG    +V  + ++L  G   H   + +A   
Sbjct: 146 FPVDVSTAAQCTIGGMAGNNSCGSRSIEYGNMVHNVDAIDAILADGSEAHFASLREA--- 202

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

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

Query: 314 VDSKVLMLAMKDIVWHSV-AEYFPADPERPTLGINLVEFCG-DEPAEVNAKVQAFIQHLQ 371
           VD  ++ LAM +  +  V  +    +P+     I LVEF G D  A++ +  Q  +  L 
Sbjct: 320 VDRTMIDLAMSNPAFRPVIGKALVGEPQ----AILLVEFAGEDRDAQLASLKQ--LTELM 373

Query: 372 SDTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPPEQLADYI 431
           +D  +      + +  E    ++ +RK  + ++ +++G+ +P  F+ED AVP E LA+Y 
Sbjct: 374 ADLGLPDSVVEMPDANEQ-KALWEVRKAGLNIMMSMKGDGKPVSFIEDCAVPLEHLAEYT 432

Query: 432 ADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALTKRYGGLL 491
           +    +   +G     + H   G LHVRP LDM+    A  ++ I+D  AAL + Y G  
Sbjct: 433 SRLTEVFHRHGTEGTWYAHASVGTLHVRPILDMRRD-GAQKMRAIADEAAALVREYKGAY 491

Query: 492 WGEHGKGL-RSEYVPEYFG-ELYPALQRLKGAFDPHNQLNPGKICTP--LGSAEGLTPVD 547
            GEHG GL R E+V   +G  L  A   +K  FDP N+ NP KI  P  +  A       
Sbjct: 492 SGEHGDGLCRGEWVAWQYGPRLNQAFSEIKALFDPDNRFNPDKIVRPPKMDDARNFRFAP 551

Query: 548 GVTLRGDLDRTIDERVW----------QDFPSAVH------------CNGNGACYNYDPN 585
           G      +D  +D   W          +  P + +            CN NG C  +D  
Sbjct: 552 GYK-EHRIDTALDWSAWNVERDPLTGQESLPGSGNDLAGGLAKAVEMCNNNGHCRKFDAG 610

Query: 586 DAMCPSWKATRERQHSPKGRASLMREWLRLQGEANIDVLAAARNKVSWLKGLPARLRNNR 645
             MCPS++ T++ QH  +GRA+ +R  L + G+     LA                    
Sbjct: 611 -TMCPSYRVTKDEQHVTRGRANTLR--LAISGQLGEAGLA-------------------- 647

Query: 646 ARNQGQEDFSHEVYDAMAGCLACKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLI 705
                    S EV + +  C++CK C   CP  V++  F+         R+   LRD L+
Sbjct: 648 ---------SDEVKETLDLCVSCKGCKRDCPTGVDMAKFKIEARAARVKRHGLRLRDKLV 698

Query: 706 GSLEFTIPYLAHAPGLYNAVMGSKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMAT 765
             +       +  PGL         +S  L   VG      + RF         +  +A 
Sbjct: 699 AFMPRYASTASRMPGLMALADNVPVLSAWLKRSVGFAPERSLPRFK--------KSFLAD 750

Query: 766 VPALRELTPAQRERSIVLVQDAFTRYFETPLLSAFIDLAHRLGHRVFLAPYSAN-----G 820
             + R        + +VL  D F    E     A   +    G+ V             G
Sbjct: 751 AVSSRNAAQGAELKEVVLFVDTFNNNMEPENARAAQQVLEAAGYTVHFNTRQGERPVCCG 810

Query: 821 KPLHVQGFLGAFAKAAIRNATQLKALADCGVPLVGLDPAMTLVYRQEYQKVPGLEGCPKV 880
           +     G +    + A R     K   + GVP+VGL+P+  L  R E+    G     + 
Sbjct: 811 RTFLAAGLVDEAKQEARRMLDLFKPFVERGVPVVGLEPSCLLSLRDEFLHY-GFGDEAQR 869

Query: 881 LLPQEWLMD---VLPEQA--------PAAPGSFRLMAHCTEKTNVPASTRQWEQVFARLG 929
           L  Q +L +   V  E+A        P A     +  HC +K    A T     +     
Sbjct: 870 LSKQAFLFEEFLVREEKAGRLELALKPLAKQQALVHGHCHQKA-FDAFTPVQTVLKWIPE 928

Query: 930 LKLVTEATGCCGMSGTYGHEARNQETSRTIFEQSW---ATKLDKDGEPLATGYSCRSQV 985
           LK+ T  + CCGM+G++G+EA +  TS+ + E S      K+D D   +A G SCR Q+
Sbjct: 929 LKVSTVESSCCGMAGSFGYEAEHYATSQAMAELSLLPAVRKMDGDTLMVADGTSCRHQI 987


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: 2296
Number of extensions: 123
Number of successful extensions: 14
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 5
Number of HSP's successfully gapped: 2
Length of query: 1006
Length of database: 1007
Length adjustment: 45
Effective length of query: 961
Effective length of database: 962
Effective search space:   924482
Effective search space used:   924482
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)
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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