GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Paraburkholderia bryophila 376MFSha3.1

Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate H281DRAFT_03360 H281DRAFT_03360 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>FitnessBrowser__Burk376:H281DRAFT_03360
          Length = 493

 Score =  388 bits (996), Expect = e-112
 Identities = 204/475 (42%), Positives = 285/475 (60%), Gaps = 2/475 (0%)

Query: 6   YTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKV 65
           Y +  +LI G W  A +      +NPAT + +G +  A  A +  A+ AA     A RK+
Sbjct: 7   YREHGMLIAGRWQSATADNGQVSINPATEERLGYMPLATPAQVTEAIDAATEASAAMRKL 66

Query: 66  PAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVY 125
              ER A +R+AA L+RERA  +A+++  E GKP+ +A  E  ++A+ I+WFADE RRV+
Sbjct: 67  TPWERTALLRRAATLIRERAPQLARIVALETGKPIAQATGEANASAESIDWFADEARRVF 126

Query: 126 GRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPA 185
           G     R  G +  V  EP+G VAAFTPWNFP+  + RK+  ALA G + +++   E   
Sbjct: 127 GMSYESRVKGGRYLVHYEPLGVVAAFTPWNFPLLLLARKMGPALAAGNAIVIRPSNEAAG 186

Query: 186 SPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGL 245
           +   L+R FVDAG P G + LV G    I+  ++  P + K++FTGS P+G+Q+  ++  
Sbjct: 187 ATMGLVRCFVDAGFPEGAVNLVIGKADAITPTVMADPRVAKISFTGSVPIGRQIVEMSAK 246

Query: 246 HMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTR 305
            +K+ TMELGGHAPVIV  DAD+      A   KFRNAGQVC SPTRF +H SI D+  +
Sbjct: 247 TLKKVTMELGGHAPVIVHRDADIDAFAHLASLGKFRNAGQVCASPTRFYIHESIFDKTVK 306

Query: 306 ALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGN- 364
           ALV+ +  L+VG+ L++ T LG L   +R  A+  ++D A   GAS+  GG R    G  
Sbjct: 307 ALVERSTALRVGDPLQQNTDLGPLTTSKRREAIERLVDEAVSEGASVLCGGRRPSQFGRG 366

Query: 365 -FFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFAN 423
            F+ PT+I+N      + N+EPFGPV  +  F  ++E I EANRLPF LA Y FTRS  N
Sbjct: 367 WFYEPTLISNPAPHIGLMNDEPFGPVGTLNRFTTMDEVITEANRLPFALAAYVFTRSMRN 426

Query: 424 VHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478
               T+RL+ G++ +N       E PFGG KDSG+G EGGP A+  YL TK + +
Sbjct: 427 TLETTERLQAGVVGVNTFVASTAETPFGGSKDSGFGREGGPNAIRDYLDTKFINL 481


Lambda     K      H
   0.318    0.134    0.393 

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: 670
Number of extensions: 28
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: 481
Length of database: 493
Length adjustment: 34
Effective length of query: 447
Effective length of database: 459
Effective search space:   205173
Effective search space used:   205173
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 (21.7 bits)
S2: 52 (24.6 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