GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Photobacterium gaetbulicola Gung47

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_044620724.1 H744_RS01660 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>NCBI__GCF_000940995.1:WP_044620724.1
          Length = 482

 Score =  336 bits (862), Expect = 9e-97
 Identities = 187/473 (39%), Positives = 259/473 (54%), Gaps = 8/473 (1%)

Query: 8   DTQLL-----IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAW 62
           D QLL     + G WV A       V NP+TG+ I  V   G  +   A+ AA      W
Sbjct: 5   DPQLLKQACYVAGNWVTAIDDACSSVTNPSTGELIATVPALGKQETSSAIHAADKAQGDW 64

Query: 63  RKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGR 122
               A ERA  +R+   L+ E  + +A ++T EQGKPL EA+ E+  AA  +EW+A+E +
Sbjct: 65  AARTAKERATVLRRWYELIVENTEDLATILTSEQGKPLAEAKGEITYAASFVEWYAEEAK 124

Query: 123 RVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEE 182
           R YG ++P     A+  V K+P+G V A TPWNFP   + RK   A A GC+ ++K   +
Sbjct: 125 RAYGELIPSHKPDARILVSKQPIGVVGAITPWNFPAAMITRKCGPAFAAGCAVVLKPAPD 184

Query: 183 TPASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASL 242
           TP +  AL      AG+PAG+  ++ GD   I   L   P ++K++FTGST VGK L S 
Sbjct: 185 TPLTALALAELAGRAGIPAGLFSVITGDAVAIGGALTESPTVKKISFTGSTGVGKLLMSQ 244

Query: 243 AGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDE 302
           +   +K+  +ELGG+AP IV +DAD+  A+     AKFRNAGQ CI   R  VHNSI DE
Sbjct: 245 SADTVKKLALELGGNAPFIVCDDADLDKAIDGVMIAKFRNAGQTCICANRIYVHNSIYDE 304

Query: 303 FTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSE 362
           F   LV   + LKV +G E G  LG L N   +  + + +D+A+  GA +  G  +   E
Sbjct: 305 FAAKLVDRVKALKVADGFEPGANLGPLINAAAVEKVQAHVDDAQAKGAKLAYGEPQ--PE 362

Query: 363 G-NFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSF 421
           G +FF P V+  +     +   E FGPVAA+  F    + I  AN    GLA YA+T+S 
Sbjct: 363 GTHFFPPQVLTEMDDTMRIATEETFGPVAALFRFSDDADVIRRANHTSSGLAAYAYTQSL 422

Query: 422 ANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474
           +     ++ LE GM+ IN+        PFGGVK+SG G EG  + +E +L TK
Sbjct: 423 SRAFKFSEALEYGMVGINEGLISTEAAPFGGVKESGLGREGARQGMEDFLETK 475


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: 547
Number of extensions: 24
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: 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 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