GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_03278
          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.

Links

Downloads

Related tools

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:

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. 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:

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:

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