GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Dyella japonica UNC79MFTsu3.2

Align Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 (characterized)
to candidate N515DRAFT_4232 N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase

Query= SwissProt::P9WNX9
         (457 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4232
          Length = 1074

 Score =  144 bits (362), Expect = 2e-38
 Identities = 140/473 (29%), Positives = 189/473 (39%), Gaps = 29/473 (6%)

Query: 3    IATINPATG-ETVKTFTAATDDEVDAAIARAHRRFADYRQTSFAQRARWANATADLLEAE 61
            +   NPA   + V ++ +A    V+ A+A A      + +   A RA      A+ LEA 
Sbjct: 596  VQVTNPADRRQVVGSYVSADSATVEKALANAVAAQHGWDRLPAASRAAILEHAAEQLEAR 655

Query: 62   ADQAAAMMTLEMGKTLAAAKAEALKCAKGFRYYAENAEALLADEPADAAKVGASAAY--- 118
              +  A+   E GK L  A AE  + A   RYYA  A              G S      
Sbjct: 656  RGEFIALCVREAGKGLPDAIAEIREAADFLRYYATMARRYFGQPEQLPGPTGESNQLFLN 715

Query: 119  GRYQPLGVILAVMPWNFPLWQAVRFAAPALMAGNVGLLKHASNVPQCALYLADVIARGGF 178
            GR    GV + + PWNFPL   +   A AL AGN  + K A            ++   G 
Sbjct: 716  GR----GVFVCISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTSLIGHAAVQLLHEAGV 771

Query: 179  PDGCFQTLLVSSGAVEAIL-RDPRVAAATLTGSEPAGQSVG---AIAGNEIKPTVLELGG 234
            P    Q L      V A L RDPRVA    TGS     ++    A     I   + E GG
Sbjct: 772  PADVLQYLPGDGATVGAALTRDPRVAGVAFTGSTETAWAINRALAARNAPIAALIAETGG 831

Query: 235  SDPFIVMPSADLDAAVSTAVTGRVQNNGQSCIAAKRFIVHADIYDDFVDKFVARMAALRV 294
             +  I   SA  +  V  AV+   Q+ GQ C AA+   V  DI D         MA L+V
Sbjct: 832  QNAMIADSSALPEQIVKDAVSSAFQSAGQRCSAARVLYVQEDIADKVCAMLAGAMAELKV 891

Query: 295  GDPTDPDTDVGPLATEQGR----NEVAKQVEDAAAAGAVIRCGGKRLDRPGWFYPPTVIT 350
            GDP    TDVGP+  E  R    +  A+  ++A   G V           G F+ P    
Sbjct: 892  GDPAQLSTDVGPVIDEDARKILVDHAARMDQEAKKIGEVAL--DPATTGNGTFFAPRAYE 949

Query: 351  DISKDMALYTEEVFGPVASVFR--AANIDEAVEIANATTFGLGSNAWTRDETEQRRFIDD 408
                 +A  T E+FGPV  V R   + +D+ V+  NAT +GL     +R +         
Sbjct: 950  --IPGLATLTREIFGPVLHVIRWKGSELDKVVDEINATGYGLTLGIHSRIDDTVEFIQSR 1007

Query: 409  IVAGQVFIN----GMTVSYPELPFGGVKRSGYGRELSA-HGIREFCNIKTVWI 456
               G  ++N    G  V     PFGG   SG G +    H +  F   +T+ I
Sbjct: 1008 ARVGNCYVNRNQIGAVVGVQ--PFGGEGLSGTGPKAGGPHYLFRFAGERTLTI 1058


Lambda     K      H
   0.319    0.133    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: 880
Number of extensions: 45
Number of successful extensions: 5
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: 457
Length of database: 1074
Length adjustment: 39
Effective length of query: 418
Effective length of database: 1035
Effective search space:   432630
Effective search space used:   432630
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: 54 (25.4 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