GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lhgD in Caulobacter crescentus NA1000

Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate CCNA_03278 CCNA_03278 aminobutyraldehyde dehydrogenase

Query= SwissProt::Q9LES4
         (483 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03278 CCNA_03278 aminobutyraldehyde
           dehydrogenase
          Length = 372

 Score =  288 bits (737), Expect = 2e-82
 Identities = 167/400 (41%), Positives = 224/400 (56%), Gaps = 39/400 (9%)

Query: 81  DTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSLKAK 140
           D VV+GAG VGLA    LS RG  V +L+     G   SSRNSEV+H G+YYP  SLKAK
Sbjct: 7   DVVVVGAGAVGLACGYALSRRGLVVAVLEEQGRIGEGVSSRNSEVIHGGLYYPTGSLKAK 66

Query: 141 FCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLEGFE 200
            CV+GR  LY +C  +++P+KK GKL+VAT   EI +LD +      N V G+  L G +
Sbjct: 67  LCVQGRRALYAFCDAHKVPYKKCGKLVVATSEDEIARLDTIWEQALANDVEGMERLTGAQ 126

Query: 201 AMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNHATF 260
           A  +EP L    ALLSPESG+  +H +ML+L                  QGE +      
Sbjct: 127 ARALEPGLNAHAALLSPESGVFASHDYMLAL------------------QGEIEA----- 163

Query: 261 SYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKRLHG 320
           +   VVL+   E  +    +A   F      AE   +L   L+V + GL +QA+A R+ G
Sbjct: 164 AGGAVVLSTPFEGAEP---LAGGGFRVRAGGAEPT-DLTCRLLVTAPGLSSQAVAGRIEG 219

Query: 321 LDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPDVEW 380
                +P +H+ +G YF LSG    PF +L+YP P  G LG H   D+ G   FGPD+E+
Sbjct: 220 YPAEQIPKAHFGKGIYFRLSG--KAPFQRLIYPPPIHGALGTHYRNDMGGQAVFGPDLEY 277

Query: 381 IECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPKQSP 440
           +   D          Y V+P +++ F   IRK++PDL    L P Y+G+RPKL GP +  
Sbjct: 278 VAAPD----------YSVDPAKADAFAAYIRKFWPDLPADRLVPDYAGVRPKLHGPGEPQ 327

Query: 441 ADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHIANK 480
            DF ++G E HG+ GL+ LFGIESPGLTSSLAI E +A +
Sbjct: 328 PDFQLRGVEDHGLAGLMALFGIESPGLTSSLAIGETVAER 367


Lambda     K      H
   0.318    0.136    0.401 

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: 503
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 483
Length of database: 372
Length adjustment: 32
Effective length of query: 451
Effective length of database: 340
Effective search space:   153340
Effective search space used:   153340
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 (21.7 bits)
S2: 51 (24.3 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, the preprint on GapMind for carbon sources, 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