GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Pseudomonas fluorescens FW300-N2E3

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 AO353_28230 AO353_28230 succinate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_28230 AO353_28230
           succinate-semialdehyde dehydrogenase
          Length = 485

 Score =  348 bits (893), Expect = e-100
 Identities = 191/463 (41%), Positives = 266/463 (57%), Gaps = 1/463 (0%)

Query: 13  IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAA 72
           IDG+W+ A +  T+DV++PA G+ + RV      +  RA+ AA+  + AWR  PA ERAA
Sbjct: 18  IDGQWIGADNAATLDVIDPANGQLLARVPAMQGTETRRAIDAAEKAWPAWRARPAAERAA 77

Query: 73  TMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPR 132
            + +    + +  D +A +MT EQGKPL EA+ E+   A  ++WFA+E RRVYG  +P  
Sbjct: 78  LLERWYQAMIDNLDDLALIMTCEQGKPLNEAKGEIRYGAGFVKWFAEEARRVYGETIPAP 137

Query: 133 NLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLR 192
           +   +   +K+PVG  AA TPWNFP   + RK + ALA GC  +VK  + TP S  AL  
Sbjct: 138 SGDRRLLTLKQPVGVCAAITPWNFPNAMITRKCAPALAAGCPIIVKPSDLTPLSALALAV 197

Query: 193 AFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATM 252
                G+PAGV  ++ G PA I   L  +P +RK++FTGST VG+ L   +  H+KR ++
Sbjct: 198 LAERVGIPAGVFNVLTGMPAGIGEELTGNPSVRKISFTGSTAVGRLLMRQSAEHIKRLSL 257

Query: 253 ELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAE 312
           ELGG+AP IV +DAD+  AV     +KFRNAGQ C+   R LV + I + F + LV+   
Sbjct: 258 ELGGNAPFIVFDDADLEQAVAGIMLSKFRNAGQTCVCANRILVQDGIYERFAQRLVEEVG 317

Query: 313 GLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIA 372
            LKVGNGL+   T+G L NP  ++ +A  ID+A   GA +  GG   G +  F  PTV+ 
Sbjct: 318 KLKVGNGLDADVTIGPLINPAAVSKVARHIDDALSQGARLLCGGIPEG-DSQFVQPTVLG 376

Query: 373 NVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLE 432
           +      + N E FGPVA +  F +  EA+A AN  P+GL  Y FT+         + LE
Sbjct: 377 DAHAGMLLANEETFGPVAPLMRFTEEAEALALANATPYGLGAYYFTQDLRRSWRFGEALE 436

Query: 433 VGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKS 475
            GM+ +N         PFGG+K SG G EG    L+ YL  K+
Sbjct: 437 FGMVGLNTGIISMEVAPFGGIKQSGLGREGSKYGLDEYLEVKA 479


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: 665
Number of extensions: 33
Number of successful extensions: 3
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: 485
Length adjustment: 34
Effective length of query: 447
Effective length of database: 451
Effective search space:   201597
Effective search space used:   201597
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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