GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Geotalea uraniireducens Rf4

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 WP_011937057.1 GURA_RS00565 NADP-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>NCBI__GCF_000016745.1:WP_011937057.1
          Length = 484

 Score =  371 bits (953), Expect = e-107
 Identities = 204/465 (43%), Positives = 274/465 (58%)

Query: 10  QLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHE 69
           Q  I+G+WVDA +G+TI V NPATG+ IG +   G ++  RA+ AA + + AWR   A E
Sbjct: 13  QCHINGQWVDADNGETIAVTNPATGETIGAIPKMGASETRRAIEAANAAYPAWRAKTAAE 72

Query: 70  RAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIV 129
           R+A +R+   L+ E  + +A LMT EQGKPL EAR E+  AA  +EWFA+EG+RVYG  +
Sbjct: 73  RSAVLRRWFELLLENQEDLAVLMTAEQGKPLAEARGEITYAASFLEWFAEEGKRVYGDTI 132

Query: 130 PPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAA 189
           P      +  V+KEP+G  AA TPWNFP   + RK   ALA GC  +VK   +TP S  A
Sbjct: 133 PQHQPDKRIVVIKEPIGVCAAITPWNFPAAMITRKAGPALAVGCPMVVKPATQTPFSALA 192

Query: 190 LLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKR 249
           L      AGVPAGV  +V G    I   +  +P++RK+TFTGST +GK L       +K+
Sbjct: 193 LAELAARAGVPAGVFNVVTGASGAIGGEMTGNPIVRKLTFTGSTEIGKLLMVQCAGTVKK 252

Query: 250 ATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVK 309
             MELGG+AP IV  DAD+  AV+ A  +K+RN GQ C+   RFLV N I D+F   LV+
Sbjct: 253 LAMELGGNAPFIVFNDADLDAAVEGALISKYRNTGQTCVCTNRFLVQNGIYDDFAAKLVE 312

Query: 310 HAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPT 369
             E LKVG+GL+  T  G L + + +  +   I +A   GA +  GG+R     +FF PT
Sbjct: 313 AVEKLKVGDGLKGETQQGPLIDLKAVEKVEEHITDAIAKGARVLCGGKRHELGRSFFQPT 372

Query: 370 VIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQ 429
           V+A+V  D  V   E FGPVA +  F   EEAI  AN   FGLA Y ++R    V  + +
Sbjct: 373 VLADVTGDMAVAREETFGPVAPLFRFSTEEEAIRMANDTEFGLAAYFYSRDIGRVWRVAE 432

Query: 430 RLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474
            +E G++ IN         PFGGVK+SG+G EG    ++ +L  K
Sbjct: 433 AVEYGIVGINTGLISTAVAPFGGVKESGFGREGSKYGVDDFLEIK 477


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: 621
Number of extensions: 20
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: 484
Length adjustment: 34
Effective length of query: 447
Effective length of database: 450
Effective search space:   201150
Effective search space used:   201150
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 Apr 09 2024. 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