GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Desulfovibrio vulgaris Hildenborough

Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate 209413 DVU0477 isocitrate dehydrogenase, NADP-dependent

Query= SwissProt::Q02NB5
         (418 letters)



>MicrobesOnline__882:209413
          Length = 380

 Score =  431 bits (1107), Expect = e-125
 Identities = 218/384 (56%), Positives = 282/384 (73%), Gaps = 12/384 (3%)

Query: 33  FIEGDGIGVDISPVMIKVVDAAVEKAYKGERKIAWMEVYAGEKATQVYDQDTWLPQETLD 92
           +IEGDGIG ++      V+DAAVEK+Y   R I W E+ AGEKA +  +   +LPQ TLD
Sbjct: 7   WIEGDGIGPEVWKAARPVIDAAVEKSYGDSRSIEWKELLAGEKAHR--ETGEYLPQSTLD 64

Query: 93  AVRDYVVSIKGPLTTPVGGGIRSLNVALRQQLDLYVCQRPVRWFEGVPSPVKKPGDVDMV 152
            +    ++IKGPL TPVG G RSLNV +RQ LDLY C RP+R+F+G+ SPVK+P  VDMV
Sbjct: 65  TLATAELAIKGPLGTPVGKGFRSLNVTMRQTLDLYACIRPIRYFDGIMSPVKRPDLVDMV 124

Query: 153 IFRENSEDIYAGVEWKAGSPEAEKVIKFLTEEMGVKKIRFTENCGIGIKPVSQEGTKRLV 212
           +FREN+ED+YAG+E++AG+PEA+++I FL +E+G K         +GIKP++++G+KRLV
Sbjct: 125 VFRENTEDVYAGIEYRAGTPEAKRLIAFLRDELGAK---VDIEAAVGIKPMTEKGSKRLV 181

Query: 213 RKALQYAVDNDRSSVTLVHKGNIMKFTEGAFKDWGYEVARDEFGAELLDGGPWMQFKNPK 272
           R+AL++A+D  R ++TLVHKGNIMKFTEG F++WGYEVARDEF A+L         +   
Sbjct: 182 RRALRFAIDQKRPNLTLVHKGNIMKFTEGGFREWGYEVARDEF-ADLTTT------ETEG 234

Query: 273 TGKNVVVKDVIADAMLQQILLRPAEYDVIATLNLNGDYLSDALAAEVGGIGIAPGANLSD 332
           T   +VVKD IADAM Q++L+RP +Y VIAT NLNGDY+SDALAA+VGG+G+APG N+SD
Sbjct: 235 TAGRLVVKDRIADAMFQEVLIRPQQYSVIATSNLNGDYISDALAAQVGGLGLAPGVNMSD 294

Query: 333 SVAMFEATHGTAPKYAGQDKVNPGSLILSAEMMLRHMGWTEAADLIIKGTNGAIAAKTVT 392
           S+A FEATHGTAP  AGQDK NPGSLIL   +ML HMGW EAA+ I K  N AIA++ VT
Sbjct: 295 SLAFFEATHGTAPTIAGQDKANPGSLILCGALMLEHMGWNEAAERIYKAVNEAIASRRVT 354

Query: 393 YDFERLMDGATLLSCSEFGDAMIA 416
            D    M+ AT +    FGD + A
Sbjct: 355 VDLATQMENATTVGTVAFGDIVTA 378


Lambda     K      H
   0.317    0.135    0.397 

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: 507
Number of extensions: 22
Number of successful extensions: 4
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: 418
Length of database: 380
Length adjustment: 31
Effective length of query: 387
Effective length of database: 349
Effective search space:   135063
Effective search space used:   135063
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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