GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lhgD in Herbaspirillum seropedicae SmR1

Align L-2-hydroxyglutarate dehydrogenase (EC 1.1.99.2) (characterized)
to candidate HSERO_RS21645 HSERO_RS21645 hydroxyglutarate oxidase

Query= BRENDA::Q9H9P8
         (463 letters)



>FitnessBrowser__HerbieS:HSERO_RS21645
          Length = 402

 Score =  314 bits (805), Expect = 3e-90
 Identities = 168/409 (41%), Positives = 243/409 (59%), Gaps = 16/409 (3%)

Query: 53  IVGGGIVGLASARALILRHPSLSIGVLEKEKDLAVHQTGHNSGVIHSGIYYKPESLKAKL 112
           ++GGGI GLA AR L+L  P + + V EKE+ +A HQ+ HNSGV+H+G+YY+P  LKA L
Sbjct: 8   VIGGGINGLAVARQLLLDDPDVRVTVFEKEEAVAQHQSSHNSGVVHAGLYYEPGGLKATL 67

Query: 113 CVQGAALLYEYCQQKGISYKQCGKLIVAVEQEEIPRLQALYEKGLQNGVPGLRLIQQEDI 172
           C +G  L+  YC+Q  + Y +CGK++VA+ +EE+PRL+A+Y K L NGVP + +I    +
Sbjct: 68  CRRGVELVKRYCEQNALPYDECGKVVVALGEEELPRLEAIYRKALANGVPDVEMIDAARL 127

Query: 173 KKKEPYCRGLMAIDCPHTGIVDYRQVALSFAQDFQEAGGSVLTNFEVKGIEMAKESPSRS 232
           ++ EP C GL A+  P T IV Y Q+A   AQ+ +E GG++  N  V+          R 
Sbjct: 128 REIEPNCVGLRALYSPRTAIVSYGQIAQRMAQEIEERGGTIRLNASVR----------RV 177

Query: 233 ID-GMQYPIVIKNTKGEEIRCQYVVTCAGLYSDRISELSGCTPDPRIVPFRGDYLLLKPE 291
           I+ G Q  I +++ +         + C+GL SDR+++ SG    PRIVPF G Y ++   
Sbjct: 178 IERGDQVHIELQSGEMHPEAFDSAIACSGLQSDRLAQQSGDAATPRIVPFFGQYYVIDEA 237

Query: 292 KCYLVKGNIYPVPDSRFPFLGVHFTPRMDGSIWLGPNAVLAFKREGYRPFDFSATDVMDI 351
               VKG IYPVPD RFPFLGVHFT R+DG + +GPNA ++  RE Y    FS  D+ D 
Sbjct: 238 YKSHVKGLIYPVPDPRFPFLGVHFTKRIDGQMTIGPNAFISLGRENYHGDRFSLRDIADY 297

Query: 352 IINSGLIKLASQNFSYGVTEMYKACFLGATVKYLQKFIPEITISDILRGPAGVRAQALDR 411
           +   G  K AS+N    + E+         V+   +++P +    +     G+RAQA++ 
Sbjct: 298 LSYPGFWKFASRNVPATLRELKTVVSERIFVREAARYVPALAEVGVTPAVRGIRAQAMES 357

Query: 412 DGNLVEDFVFDAGVGDIGNRILHVRNAPSPAATSSIAISGMIADEVQQR 460
           +G LV+DFV         +R+ H+RNAPSP ATSS+AI   I   + +R
Sbjct: 358 NGRLVDDFVIRQ-----SSRVTHIRNAPSPGATSSLAIGEHIVRNLIRR 401


Lambda     K      H
   0.321    0.140    0.420 

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: 481
Number of extensions: 19
Number of successful extensions: 2
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: 463
Length of database: 402
Length adjustment: 32
Effective length of query: 431
Effective length of database: 370
Effective search space:   159470
Effective search space used:   159470
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: 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 (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