GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lhgD in Marinobacter algicola DG893

Align L-2-hydroxyglutarate dehydrogenase (EC 1.1.99.2) (characterized)
to candidate WP_007154818.1 MDG893_RS15820 NAD(P)/FAD-dependent oxidoreductase

Query= BRENDA::Q9H9P8
         (463 letters)



>NCBI__GCF_000170835.1:WP_007154818.1
          Length = 371

 Score =  143 bits (361), Expect = 8e-39
 Identities = 127/411 (30%), Positives = 194/411 (47%), Gaps = 54/411 (13%)

Query: 50  DIVIVGGGIVGLASARALILRHPSLSIGVLEKEKDLAVHQTGHNSGVIHSGIYYKPESLK 109
           D V++G GIVGLA ARAL ++     + VLE         +  NS VIH+GIYY  +SLK
Sbjct: 10  DTVVIGAGIVGLAVARALAMQ--GREVLVLESGAHFGEGVSSRNSEVIHAGIYYPEDSLK 67

Query: 110 AKLCVQGAALLYEYCQQKGISYKQCGKLIVAVEQEEIPRLQALYEKGLQNGVPGLRLIQQ 169
           A+LCV+G  +LYEYCQ +GI++++ GK IVA    ++ RL  +  + L+NGVP L+ + +
Sbjct: 68  ARLCVRGRRMLYEYCQTRGINHRRSGKWIVANGVSQVERLDTIASQALRNGVP-LQRVTR 126

Query: 170 EDIKKKEPYCRGLMAIDCPHTGIVDYRQVALSFAQDFQEAGGSVLTNFEVKGIEMAKESP 229
             ++   P      A+  P TGIVD   V LS   DF+  GG ++    V+ + +     
Sbjct: 127 RALQVSLPDVTAQEALYSPETGIVDSHGVMLSLLGDFEGHGGQLVCQAPVE-LAVTGHGE 185

Query: 230 SRSIDGMQYPIVIKNTKGEEIRCQYVVTCAGLYSDRI-SELSGCTPD--PRIVPFRGDYL 286
            R   G Q P         E+R Q VV  AGL +  + +   G   D  PR    RG Y 
Sbjct: 186 HRLWIGGQAPC--------ELRAQRVVNAAGLGAVPLATSWEGVPADIVPRQWLARGVYF 237

Query: 287 LLKPEKCYLVKGNIYPVPDSRFPFLGVHFTPRMDGSIWLGPNAVLAFKREGYRPFDFSAT 346
                  +  K  +YP+P+S    LGVH T  + G    GP+ V   +RE     DFS  
Sbjct: 238 SYSGHHPF--KSLVYPIPES--GGLGVHLTLDLAGQARFGPD-VEWIERE-----DFS-- 285

Query: 347 DVMDIIINSGLIKLASQNFSYGVTEMYKACFLGATVKYLQKFIPEITISDILRGPAGVRA 406
                 ++ G  K  + +                    ++++ P +  S +    AG+R 
Sbjct: 286 ------VDPGRAKSFANS--------------------IRRWWPALDESRLKPAYAGIRP 319

Query: 407 QALDRDGNLVEDFVFDAGVGDIGNRILHVRNAPSPAATSSIAISGMIADEV 457
           + L  DG    DF            ++H+    SP  T+++AI+  +A+++
Sbjct: 320 KLLGPDGGF-SDFRIAGECRHGVPGLVHLFGIESPGLTAALAIADEVAEQL 369


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: 414
Number of extensions: 23
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: 371
Length adjustment: 31
Effective length of query: 432
Effective length of database: 340
Effective search space:   146880
Effective search space used:   146880
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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