GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Streptacidiphilus oryzae TH49

Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate WP_051940857.1 BS73_RS27490 aldehyde dehydrogenase

Query= SwissProt::D4GP41
         (482 letters)



>NCBI__GCF_000744815.1:WP_051940857.1
          Length = 481

 Score =  324 bits (831), Expect = 4e-93
 Identities = 193/464 (41%), Positives = 261/464 (56%), Gaps = 9/464 (1%)

Query: 23  EVTNPANPSEVVAAYQHSNENDAAAAVDAAVAAEDE--WRNTPGPERGRILREAGTLLAQ 80
           ++ NPAN  EV+A  + ++     AAV  A  A D   W       RGRI+   G L+  
Sbjct: 5   KIVNPAN-GEVLAVVEETDVQGVEAAVARAKEAYDSGRWSGLDASRRGRIVSSVGDLMLA 63

Query: 81  RKDELTEILTAEEGKARPEAAGEVQRAIDIFHYFSSKAADLGGTKKGASGPNTNLYTRQE 140
             +EL  + +   GK   +   EV+ A   FHY+   A  L G      G   N+  RQ 
Sbjct: 64  HLEELAVLESGSNGKPVRDTRKEVESAARTFHYYGGLADKLQGDVIPVDGKYLNIAVRQ- 122

Query: 141 PVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIAPGVVIEIARALDEAGLPDGV 200
           P+GVAAL+ PWN P+ + +WKLAPAL AGNT VLKP+   P   + +A  L E  +P GV
Sbjct: 123 PLGVAALLLPWNSPLLLLSWKLAPALVAGNTAVLKPSEFTPLSTLRLAELLAETEIPAGV 182

Query: 201 LNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQATDAGKRVQTELGGKNPTLVA 260
           +NVVTG G  VG+  + +     VSF+G    G  +  +A D  KRV  ELGGK+  +V 
Sbjct: 183 VNVVTGLGDPVGAALVRSANVAKVSFSGCVGTGRAIAAEAGDGLKRVNLELGGKSANIVF 242

Query: 261 DSANPAEAADIVANGGFGTTGQSCTACSRAIVHEDVYDDFVAELVDRAESLDVGP--GTD 318
             A+   AA   A   FG  GQSC A SR +VHEDVYD+F+A  +  A  + VG     +
Sbjct: 243 PDADIRAAARSAARAAFGGAGQSCAAGSRLLVHEDVYDEFMAVFMPIARGIVVGDPLAEE 302

Query: 319 HEMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGEAVETGHFVEPTVFTDVDPDMR 378
            EMGP  +  +   T+ +I+ A  EGATL+ GGG PEGE +  G+FV PTVF DV+P MR
Sbjct: 303 TEMGPVSNAPQYEKTMAFIESARKEGATLLCGGGRPEGEGLNQGYFVAPTVFADVEPGMR 362

Query: 379 IAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVTDDHTEANRFVDEVEAGVVKVN 438
           IAQEE+FGPVV+V+     +E +A+AN V YGL+ ++ T D + A R    ++AG + VN
Sbjct: 363 IAQEEIFGPVVSVLRFGTEEEAVALANGVGYGLTGALWTADLSRALRVTQRIDAGSLWVN 422

Query: 439 DKTTGLELHVPFGGFKRSSSETWREQGDAGLDFYTIEKTVYDSY 482
                L    P+GGFK  SS   +E G  GL+ YT  K+V+ +Y
Sbjct: 423 -CYKALSPASPYGGFK--SSGYGKENGLLGLEEYTQWKSVWFNY 463


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: 573
Number of extensions: 24
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: 482
Length of database: 481
Length adjustment: 34
Effective length of query: 448
Effective length of database: 447
Effective search space:   200256
Effective search space used:   200256
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