GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Phaeo:GFF2285 PGA1_c23170
           succinate-semialdehyde dehdyrogenase GabD
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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