GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Streptacidiphilus oryzae TH49

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_084704195.1 BS73_RS19435 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>NCBI__GCF_000744815.1:WP_084704195.1
          Length = 510

 Score =  340 bits (873), Expect = 5e-98
 Identities = 189/469 (40%), Positives = 261/469 (55%), Gaps = 1/469 (0%)

Query: 11  LLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHER 70
           L I GEW  AASG    V +P+  + +  VA AG  D + A  AA +  EAW      ER
Sbjct: 39  LFIGGEWRPAASGAEFPVEDPSLARTLRTVADAGAEDAEAAAEAAGAAQEAWAATAPRER 98

Query: 71  AATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVP 130
              +R+A  L+ +R + +A LMT E GKPL EAR EV  AA+   WF++E  R+ G    
Sbjct: 99  GEILRRAYQLLLDRQEDLALLMTLEMGKPLAEARGEVAYAAEFFRWFSEEAVRIEGGYQT 158

Query: 131 PRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAAL 190
             +   +  V++ PVGPV   TPWNFP+    RK+  A+A GC+ +VK  E+TP +  AL
Sbjct: 159 SPDGRDRFIVMRRPVGPVLLVTPWNFPLAMGTRKIGPAIAAGCTMIVKPAEQTPLTMLAL 218

Query: 191 LRAFVDAGVPAGVIG-LVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKR 249
                +AGVPAGV+  L    P E+   L+   VIRK++FTGST +G+ L   +   + R
Sbjct: 219 AAIMTEAGVPAGVLNVLTTNRPGEVVEPLLRGGVIRKLSFTGSTAIGRLLLEQSAQQVLR 278

Query: 250 ATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVK 309
            ++ELGG+AP IV  DAD+  AV+ A  AK RN G+ C +  R  VH S+  EF   L  
Sbjct: 279 VSLELGGNAPFIVCADADLDKAVEGAMAAKMRNIGEACTAANRLYVHESVAAEFAERLAA 338

Query: 310 HAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPT 369
               L VG G E G  +G L +      +  ++ +A   GA + TGGE    EG F+ PT
Sbjct: 339 RMGALTVGRGTEPGVDVGPLIDEAGRGKVDELVSDAVGRGAKVLTGGEHAPGEGYFYTPT 398

Query: 370 VIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQ 429
           V+ +VP DA + + E FGPVA +  F   EEA+A AN   +GL  Y FT +      L++
Sbjct: 399 VLTDVPADAAMLSQEIFGPVAPLLAFSDDEEAVAAANDTEYGLVSYLFTENLDRALRLSE 458

Query: 430 RLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478
           RL+ GM+ +N+     P  PFGGVK SG G EGG   ++ +L T+ + V
Sbjct: 459 RLDTGMVGLNKGVVSNPAAPFGGVKHSGLGREGGRMGIDEFLETRYLAV 507


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: 648
Number of extensions: 30
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: 510
Length adjustment: 34
Effective length of query: 447
Effective length of database: 476
Effective search space:   212772
Effective search space used:   212772
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