GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Brevibacterium jeotgali SJ5-8

Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate WP_101588846.1 BJEO58_RS07395 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= SwissProt::D4GP41
         (482 letters)



>NCBI__GCF_900169175.1:WP_101588846.1
          Length = 497

 Score =  274 bits (701), Expect = 4e-78
 Identities = 171/476 (35%), Positives = 248/476 (52%), Gaps = 8/476 (1%)

Query: 7   NYVNGEWVTSETGETT-EVTNPAN--PSEVVAAYQHSNENDAAAAVDAAVAAEDEWRNTP 63
           +++NG  V    G    +V NPA    S  VA    ++ +    A+ AA  A   WR+T 
Sbjct: 6   HWINGRTVEESHGARFGDVVNPATGVSSGRVAL---ASADRGREAIQAAADAFPAWRDTS 62

Query: 64  GPERGRILREAGTLLAQRKDELTEILTAEEGKARPEAAGEVQRAIDIFHYFSSKAADLGG 123
             +R  I+     LL  RK+EL  I+TAE GK   +A GEV R +++     + +  L G
Sbjct: 63  LTKRTSIIFTFRELLNARKEELAAIITAEHGKVLSDALGEVSRGLEVVELCCNISYLLKG 122

Query: 124 TKKGASGPNTNLYTRQEPVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIAPGV 183
                +    ++++ ++PVGV+A+I+P+N+P  +P W    A+A GNTVVLKP+   P  
Sbjct: 123 GHSENASTGIDVHSVRQPVGVSAIISPFNFPAMVPLWFFPVAIATGNTVVLKPSEKDPST 182

Query: 184 VIEIARALDEAGLPDGVLNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQATDA 243
              +A    EAGLPDGV NV+ G   +V +  + +   D VSF GS+ + + +YE A+  
Sbjct: 183 ANWLAELWKEAGLPDGVFNVLHGDKEAVDT-LLTDPQVDSVSFVGSTPIAKYIYETASAH 241

Query: 244 GKRVQTELGGKNPTLVADSANPAEAADIVANGGFGTTGQSCTACSRAIVHEDVYDDFVAE 303
           GKRVQ   G KN  LV   A+    AD   N G+G  G+ C A S  +  + + D+ VA+
Sbjct: 242 GKRVQALGGAKNHMLVLPDADLDITADSAVNAGYGAAGERCMAISVVVAVDAIADELVAK 301

Query: 304 LVDRAESLDVGPGT-DHEMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGEAVETG 362
           + +R   L VG GT D +MGP ++ +       YID     GA LV  G     +A    
Sbjct: 302 IAERTRGLKVGDGTRDSDMGPLITVAHRDKVAGYIDAGVESGAELVLDGRTSTPDADSDA 361

Query: 363 HFVEPTVFTDVDPDMRIAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVTDDHTE 422
            F+ PT+F  V PDM I  +E+FGPV+ V+ V  +DEGL + N   YG   +I T+D   
Sbjct: 362 AFLNPTLFDRVTPDMSIYTDEIFGPVLVVVRVPSYDEGLDLINANPYGNGTAIFTNDGGA 421

Query: 423 ANRFVDEVEAGVVKVNDKTTGLELHVPFGGFKRSSSETWREQGDAGLDFYTIEKTV 478
           A RF +EV+ G+V VN        H  FGG+K S        G  G+ F+T  K +
Sbjct: 422 ARRFENEVQVGMVGVNVPIPVPVAHFSFGGWKNSLFGDTHAYGAEGVHFFTRGKVI 477


Lambda     K      H
   0.310    0.130    0.370 

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: 583
Number of extensions: 27
Number of successful extensions: 3
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: 482
Length of database: 497
Length adjustment: 34
Effective length of query: 448
Effective length of database: 463
Effective search space:   207424
Effective search space used:   207424
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 52 (24.6 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