GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Phaeobacter inhibens BS107

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 GFF2285 PGA1_c23170 succinate-semialdehyde dehdyrogenase GabD

Query= SwissProt::Q1JUP4
         (481 letters)



>FitnessBrowser__Phaeo:GFF2285
          Length = 474

 Score =  327 bits (838), Expect = 5e-94
 Identities = 184/473 (38%), Positives = 265/473 (56%), Gaps = 9/473 (1%)

Query: 9   TQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAH 68
           T L I+G W    + +  DV+NPAT + +  VA A IAD D AL AA++  + W      
Sbjct: 4   TDLYINGAW--HKTSERFDVINPATEEVLASVASADIADADAALDAAEAAMKDWAARTPR 61

Query: 69  ERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRI 128
           +R+  +RKA  L+ +R D  A L+T E GK  T+A+ E   AA+   WFA+E  R  G I
Sbjct: 62  QRSEVLRKAWELMTKRLDYFANLITLENGKAGTDAKGEATYAAEFFRWFAEEAVRADGMI 121

Query: 129 VPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPA 188
                 GA+  V  +P G     TPWN+P     RK++ ALA GC  ++K   ETP +  
Sbjct: 122 THAPASGARIVVQHKPAGLAVLVTPWNYPAAMGTRKIAPALAAGCGVIIKPASETPLTML 181

Query: 189 ALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPH----PVIRKVTFTGSTPVGKQLASLAG 244
           AL+    +AGVPAG++ ++   P+  +  L+ H    P IR V+FTGST VG++L   A 
Sbjct: 182 ALMPLLEEAGVPAGLVNVL---PSRKTGSLVDHMLHDPRIRVVSFTGSTGVGRKLLKGAA 238

Query: 245 LHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFT 304
             + +  MELGG+APV+V EDAD+ +A++    AK RN G+ C +  R  VH  I DEFT
Sbjct: 239 DQVLKPAMELGGNAPVVVFEDADMDVAIEGTMLAKMRNLGEACTAANRIYVHEDIADEFT 298

Query: 305 RALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGN 364
           + L      LKVG+G +    +G L N      +A+ + +A   GA +E GG     +G 
Sbjct: 299 KRLSAAMSALKVGDGTDPSVDVGPLVNADTRDKVAAFVADAVAKGAKVECGGTTPNGKGF 358

Query: 365 FFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANV 424
           ++ PTV++NV  DA+   +E FGPVAAI+ F   +E IA AN   +GL  Y F+  F   
Sbjct: 359 YYPPTVLSNVSEDAECVRDEIFGPVAAIQTFTNQDEVIARANDTEYGLVAYVFSEDFKRA 418

Query: 425 HLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVT 477
             + ++LE GM+ +N+     P  PFGGVK SG G EGG E +  ++ T+ ++
Sbjct: 419 LQVCEQLEYGMVGLNRGLVSDPAAPFGGVKQSGLGREGGHEGMLEFMETQYIS 471


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: 605
Number of extensions: 31
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: 474
Length adjustment: 34
Effective length of query: 447
Effective length of database: 440
Effective search space:   196680
Effective search space used:   196680
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: 51 (24.3 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