GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1734 Succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16)

Query= SwissProt::Q1JUP4
         (481 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1734
          Length = 480

 Score =  374 bits (961), Expect = e-108
 Identities = 198/465 (42%), Positives = 277/465 (59%), Gaps = 2/465 (0%)

Query: 10  QLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHE 69
           Q  IDG WVDA +G+TI V NPATG+ +G V   G A+  RA+ AA     AWR + A E
Sbjct: 12  QAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRGLTAKE 71

Query: 70  RAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIV 129
           RA  +R+   L+ E  D +A+LMT EQGKPL EA+ E++ AA  IEWFA+E +RVYG ++
Sbjct: 72  RANKLRRWFELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRVYGDVI 131

Query: 130 PPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAA 189
           P      +  V+K+P+G  AA TPWNFP   + RK   ALA GC+ ++K   +TP S  A
Sbjct: 132 PGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFA 191

Query: 190 LLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKR 249
           L      AG+P GV  +V G   +I S L  +P++RK++FTGST +G+QL +     +K+
Sbjct: 192 LAELAQRAGIPNGVFSVVTGSAGDIGSELTGNPIVRKLSFTGSTEIGRQLMTECAKDIKK 251

Query: 250 ATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVK 309
            ++ELGG+AP IV +DAD+  AV+ A  +K+RN GQ C+   R  + +S+ D F   L  
Sbjct: 252 VSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVYDAFAEKLKV 311

Query: 310 HAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPT 369
               LK+GNGLE+GTT G L + + +  +   I +A   GA++  GG+ +  +GNFF PT
Sbjct: 312 AVAKLKIGNGLEDGTTTGPLIDEKAVAKVQEHIADAVGKGATVLAGGKSM--QGNFFEPT 369

Query: 370 VIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQ 429
           ++ NVP +A V   E FGP+A +  F    + IA +N   FGLA Y + R    V  + +
Sbjct: 370 ILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFRVAE 429

Query: 430 RLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474
            LE GM+ +N         PFGG+K SG G EG    +E YL  K
Sbjct: 430 ALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474


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: 602
Number of extensions: 25
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: 480
Length adjustment: 34
Effective length of query: 447
Effective length of database: 446
Effective search space:   199362
Effective search space used:   199362
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