GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Novosphingobium fuchskuhlense FNE08-7

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_067907978.1 AQZ52_RS07445 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>NCBI__GCF_001519075.1:WP_067907978.1
          Length = 468

 Score =  439 bits (1130), Expect = e-128
 Identities = 232/466 (49%), Positives = 306/466 (65%), Gaps = 1/466 (0%)

Query: 11  LLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHER 70
           ++IDGE V     +T  VVNPATG+ +  +  A  ADLDRAL  AQ GF+ WR     +R
Sbjct: 1   MIIDGERVTGGGRRTHAVVNPATGETLAELPLAEAADLDRALETAQRGFKLWRNSTPQQR 60

Query: 71  AATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVP 130
           AA ++ AA L+ ER + +A++ T EQGK L EAR+EVL    +  ++A E  R+YGR + 
Sbjct: 61  AAVLQGAAKLMLERQEDLARIATMEQGKTLPEARIEVLMNVGLFNFYAGEVFRLYGRALV 120

Query: 131 PRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAAL 190
            R  G + TV  EPVGPVAAF PWNFP+    RKL A +A GCS ++KA EETPAS   +
Sbjct: 121 -RPEGMRSTVTHEPVGPVAAFAPWNFPLGNPGRKLGAPIAAGCSVILKAAEETPASALGV 179

Query: 191 LRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRA 250
           L+  +DAG+P  V   V+G P E+S +L+  P+IRK++FTGST VGK LA LA   MKR 
Sbjct: 180 LQCLLDAGLPKEVAQAVFGVPDEVSRHLLGSPIIRKLSFTGSTMVGKHLAKLAAEDMKRT 239

Query: 251 TMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKH 310
           TMELGGH PV+V  D+D+   +      K+RNAGQVC+SPTRF+V  S+ D F     + 
Sbjct: 240 TMELGGHGPVLVFGDSDLDRVLDTVVPHKYRNAGQVCVSPTRFIVEESVYDRFRSGFAER 299

Query: 311 AEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTV 370
           A+ + VGNGLEEG  +G +ANPRR  AM  +I +A   GA++ TGGERIG+ G F+AP+V
Sbjct: 300 AKAVTVGNGLEEGIRMGPMANPRRPEAMDRLIGDAVAKGATLHTGGERIGNAGYFYAPSV 359

Query: 371 IANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQR 430
           ++++PLDA + N EPFGPVA I  +   E  IAEANRLP+GLA YA+T        L + 
Sbjct: 360 LSDIPLDALIMNEEPFGPVALINRYVGEEAMIAEANRLPYGLAAYAWTSDGKRQQRLARE 419

Query: 431 LEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476
           +E GM+ IN       + PFGGV+ SG+GSE GPE +   +VTK+V
Sbjct: 420 IEAGMVGINTTMIGGADAPFGGVRWSGHGSEDGPEGVLACMVTKAV 465


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: 693
Number of extensions: 37
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: 468
Length adjustment: 33
Effective length of query: 448
Effective length of database: 435
Effective search space:   194880
Effective search space used:   194880
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 24 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