Alignments for a candidate for ydiJ in Crocosphaera subtropica ATCC 51142

GapMind for catabolism of small carbon sources

Alignments for a candidate for ydiJ in Crocosphaera subtropica ATCC 51142

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate WP_009544598.1 CCE_RS12850 FAD-linked oxidase C-terminal domain-containing protein

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



>NCBI__GCF_000017845.1:WP_009544598.1
          Length = 1005

 Score =  837 bits (2163), Expect = 0.0
 Identities = 441/999 (44%), Positives = 630/999 (63%), Gaps = 34/999 (3%)

Query: 17   FLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVARVATLMGEPRFQ 76
            FL  L+ + F G I  D A R + +TDNSIYQ LPQ  VFP   +D+  +  L  +  F+
Sbjct: 18   FLTCLKETTFSGDIKGDIANRLIASTDNSIYQILPQGVVFPRTTEDIREIFKLANKTEFE 77

Query: 77   QVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAGTVKDQLNAALKP 136
             V  +PRGGGTGTNGQSL+  I++D S++MN +LE+N+EE WVRVQ G + DQLN  L  
Sbjct: 78   SVTFSPRGGGTGTNGQSLSPSIIIDCSKYMNQVLELNLEEDWVRVQPGIILDQLNQILSE 137

Query: 137  HGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLLGGERLHSLPIDD 196
            H LFFAP L+ SNRAT+GGMINTDA+G+GS  YGKT DH+LEL  VL  G    S  I  
Sbjct: 138  HNLFFAPSLAPSNRATIGGMINTDAAGKGSRIYGKTSDHILELSWVLSNGTLSSSSQISR 197

Query: 197  AALEQACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTGYDLAHLRDE-QGRFNL 255
              L+      GR+GE+Y +  +I   +AELI+  FPKL R +TGY++A + DE +  F+L
Sbjct: 198  DDLDSLKQQNGRLGEIYNLIDKIVSEKAELIDNIFPKLTRFMTGYNVAKVYDETRNYFDL 257

Query: 256  NSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDANALMAHKPLSIETVD 315
            N +L G+EG+LG + E KL +  IPK   L+ + Y +F  AL+DA  L+ + P +IETVD
Sbjct: 258  NRILAGSEGTLGIITETKLKLTKIPKATQLLAIHYQNFDAALKDATNLLNYDPAAIETVD 317

Query: 316  SKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVNAKVQAFIQHLQSDTS 375
              +L LA  D ++  V ++           INLVEF G+   ++  ++   I  L++  +
Sbjct: 318  EIILELAKNDSIYQEVKDFI-----CEAKAINLVEFVGETNQDIEQQISPLIDQLENYKN 372

Query: 376  VERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPPEQLADYIADFR 435
               LG+   E  E + +++++RK+   LLG++ G  +P  F+EDTAV PE LA Y  +F+
Sbjct: 373  PGVLGYYHTEKPEEIKKLWSLRKKGAALLGSMPGHRKPIAFIEDTAVSPENLASYTHEFQ 432

Query: 436  ALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALTKRYGGLLWGEH 495
            ALL+ Y L Y MFGHVD G LHVRPALDMK P    L++ ISD V  L ++YGG++WGEH
Sbjct: 433  ALLNSYKLTYAMFGHVDVGCLHVRPALDMKVPEDEKLIREISDQVVNLVRKYGGVIWGEH 492

Query: 496  GKGLRSEYVPEYFG-ELYPALQRLKGAFDPHNQLNPGKICTPLGSAEGLTPVDGVTLRGD 554
            GKG RSEY P +FG ELY  L+R+K  FDP N+LNPGKI TP  S++ +  ++  TLRG 
Sbjct: 493  GKGFRSEYTPLFFGEELYQDLRRIKEVFDPDNKLNPGKIVTPYNSSDEIVKLES-TLRGH 551

Query: 555  LDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQHSPKGRASLMREWLR 614
             DR + ++   ++ +  +CNGNGAC+N++P++ +CPS K TR R HSPKGRA L+REWLR
Sbjct: 552  FDRQVSQQFRTEYEAVFNCNGNGACFNFNPDEIICPSAKQTRNRIHSPKGRAMLLREWLR 611

Query: 615  LQGEANIDVLAAARNKVSWLKGL--PARLRNNRARNQGQEDFSHEVYDAMAGCLACKSCA 672
            L  ++N         K S+ + L  P ++     + QG+EDFSH+VY+AM GCLACK C 
Sbjct: 612  LLSKSNF--------KDSFKENLSFPKKVWYTLDKWQGKEDFSHDVYEAMQGCLACKGCI 663

Query: 673  GQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPGLYNAVMGSKWVS 732
             QCPI V++PD +S+FLE YH RY R  RDYL+ ++E  I Y + AP L+N+++    +S
Sbjct: 664  SQCPIHVDIPDLKSQFLERYHSRYLRSFRDYLMANIEKLIYYQSFAPNLFNSLV-QNTIS 722

Query: 733  QLLADK-VGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERSIVLVQDAFTRY 791
            +LL +K + +VD+PLIS   +     +  + +  +  L +L+  +++ SI+L+QDAFT +
Sbjct: 723  KLLINKTLNLVDTPLIS---YPTVRDKLPIAL-NIETLDKLSVEEQKNSIILLQDAFTSF 778

Query: 792  FETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNATQLKALADCGV 851
            +E+ L+         L + V++ P+  NGK LH++GF+  F      N   LK + D  +
Sbjct: 779  YESQLVIDTYHCLENLDYNVYILPFFINGKTLHLKGFINNFKMVIHNNINALKTVLDLDI 838

Query: 852  PLVGLDPAMTLVYRQEYQKVPGLEGC-PKVLLPQEWLMDV---LPEQAPAAPGSFRLMAH 907
            P++G++P+MTL YR EY+K+   +    KV L QE+L+      P+     P  + L+AH
Sbjct: 839  PIIGIEPSMTLTYRDEYEKIASDKNIFKKVQLIQEFLVTQEKRFPKIQSTHP--YYLLAH 896

Query: 908  CTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIFEQSWATK 967
            C EK+    S +QW+ VF  +G+ L   + GCCGM+G YGHE  + E S+ I++ SW   
Sbjct: 897  CHEKSLAFNSEKQWQTVFKNMGISLNIVSVGCCGMAGMYGHEKEHYENSKGIYQSSWQQH 956

Query: 968  LDK--DGEP--LATGYSCRSQVKRMTERKMRHPLEVVLQ 1002
            L K  D +P  L TGYSCRSQVKR +  K +HP++ + Q
Sbjct: 957  LPKKIDEQPYYLVTGYSCRSQVKRFSGWKPQHPIQALNQ 995


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: 2205
Number of extensions: 63
Number of successful extensions: 10
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: 1006
Length of database: 1005
Length adjustment: 45
Effective length of query: 961
Effective length of database: 960
Effective search space:   922560
Effective search space used:   922560
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 Apr 09 2024. 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 2024 update 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