GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Caulobacter crescentus NA1000

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 CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>FitnessBrowser__Caulo:CCNA_03242
          Length = 485

 Score =  370 bits (950), Expect = e-107
 Identities = 199/475 (41%), Positives = 274/475 (57%), Gaps = 3/475 (0%)

Query: 1   MANVTYTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFE 60
           M  +   +T  LIDG+WV   +  + DV+NPA G  I  VA  G A+   A+ AA     
Sbjct: 4   MTALNLVETAALIDGQWVRGEA--SFDVLNPADGTLIAAVADLGAAETTLAIDAAHRALP 61

Query: 61  AWRKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADE 120
           AW    A ER A +R+ + L+   AD +A+LMT EQGKPL EA+ EV+  A  I+WFA+E
Sbjct: 62  AWAARTAKERGAILRRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYGASFIDWFAEE 121

Query: 121 GRRVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAP 180
            +R YG  +P    G +   +K+PVG  AA  PWNFP+  + RK+  ALA GC+ +VK  
Sbjct: 122 AKRAYGHTIPTPMPGKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPA 181

Query: 181 EETPASPAALLRAFVDAGVPAGVIGLVYGD-PAEISSYLIPHPVIRKVTFTGSTPVGKQL 239
            ETP S  A+ R   +AGVPAGV+ +V     +E+   L     +RK++FTGSTP+GK L
Sbjct: 182 AETPLSALAIARLATEAGVPAGVLNIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVL 241

Query: 240 ASLAGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSI 299
                  MK+ ++ELGG+AP IV +DAD+  AV  A  +K+RNAGQ C+   R +V + I
Sbjct: 242 YQQCAGTMKKLSLELGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGI 301

Query: 300 RDEFTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERI 359
            D F   L +    LKVG G  EG  +G L N + LT +  ++  A + GA + TGG+  
Sbjct: 302 HDAFAARLAEKVAALKVGPGTGEGVQIGPLINEKALTKVVGLVSGAVQAGAEVLTGGDVH 361

Query: 360 GSEGNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTR 419
           G  G+F+ PTV+     +  +F  E FGPVA I  F+   EA+  AN  PFGLA Y ++R
Sbjct: 362 GLGGHFYQPTVLVGATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSR 421

Query: 420 SFANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474
                  + +++E GM+ IN+        PFGGVK+SG G EG  E L+ YL TK
Sbjct: 422 DVGRCWRVAEQIEAGMVGINEGLISTEVAPFGGVKESGLGREGASEGLDEYLETK 476


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: 664
Number of extensions: 36
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.

Links

Downloads

Related tools

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