GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Klebsiella michiganensis M5al

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 BWI76_RS05620 BWI76_RS05620 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS05620 BWI76_RS05620 NAD-dependent
           succinate-semialdehyde dehydrogenase
          Length = 482

 Score =  370 bits (949), Expect = e-107
 Identities = 191/469 (40%), Positives = 274/469 (58%)

Query: 10  QLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHE 69
           Q +I+G W DA+  +T+ V NPA G+P+G V   G  +   A+ AA     AWR + A E
Sbjct: 12  QAMINGRWRDASGKETLAVTNPANGQPLGNVPKMGAGETREAIDAAARALPAWRALTAKE 71

Query: 70  RAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIV 129
           R++ +R+   L+ E  D +A+LMT EQGKPL EA+ E+  AA  IEWFA+EG+R+YG  +
Sbjct: 72  RSSILRRWFELMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKRIYGDTI 131

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

Query: 190 LLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKR 249
           L      AG+P GV  +V G  +E+   L  +P++RK++FTGST +G+QL       +K+
Sbjct: 192 LAELANRAGIPEGVFNVVTGSASEVGGELTGNPLVRKLSFTGSTEIGRQLMEQCAKDIKK 251

Query: 250 ATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVK 309
            ++ELGG+AP IV +DAD+  AV+ A  +KFRNAGQ C+   R  V +S+ D F   L +
Sbjct: 252 VSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDSVYDRFAEKLQQ 311

Query: 310 HAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPT 369
               L++G+GL+   T+G L + + +  +   I +A   GA + TGG+     GNFF PT
Sbjct: 312 AVSKLQIGDGLQPNVTIGPLIDEKAIAKVQEHIADALGKGARVVTGGKAHELGGNFFQPT 371

Query: 370 VIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQ 429
           ++ +VP DA V   E FGP+A +  F    + IA+AN   FGLA Y + R    V  + +
Sbjct: 372 ILVDVPGDAKVAKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLGRVFRVGE 431

Query: 430 RLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478
            LE G++ IN         PFGGVK SG G EG    +E YL  K + +
Sbjct: 432 ALEYGIIGINTGLISTEVAPFGGVKSSGLGREGSKYGIEDYLEIKYMCI 480


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: 613
Number of extensions: 21
Number of successful extensions: 1
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: 482
Length adjustment: 34
Effective length of query: 447
Effective length of database: 448
Effective search space:   200256
Effective search space used:   200256
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 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