GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Streptomyces kebangsaanensis SUK12

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_073952689.1 RH94_RS37005 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>NCBI__GCF_001906585.1:WP_073952689.1
          Length = 494

 Score =  355 bits (910), Expect = e-102
 Identities = 192/471 (40%), Positives = 275/471 (58%), Gaps = 1/471 (0%)

Query: 11  LLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHER 70
           L IDGEW  + SG T+ V +P T   I  VA A  AD   AL AA     +W   P  ER
Sbjct: 22  LYIDGEWRPSRSGATVAVEDPGTRTVIAEVADADTADATDALDAAVRAQASWAATPPRER 81

Query: 71  AATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVP 130
              +R+A   +  R D +A LMT E GKP  E++ EV  AA+ + WF++E  R+ G  + 
Sbjct: 82  GDVLRRAFEAIIARKDDLASLMTLEMGKPFAESQAEVAYAAEFLRWFSEEAVRIDGGYMT 141

Query: 131 PRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAAL 190
               G++   +++PVGP    TPWNFP+    RK+  ALA GC+ +VK  ++TP S  AL
Sbjct: 142 APGGGSRVVTMRQPVGPCLLVTPWNFPMAMGTRKIGPALAAGCTVVVKPAKQTPLSMLAL 201

Query: 191 LRAFVDAGVPAGVIGLVYGDPA-EISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKR 249
           +    +AG PAGV+ +   + + E++ +L+  P +RK++FTGST VG+ L + +  ++ R
Sbjct: 202 VDILREAGAPAGVVNVFTTNRSGEVTDHLLNDPRLRKLSFTGSTEVGRALLAKSSRNVLR 261

Query: 250 ATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVK 309
            +MELGG+AP +V  DAD+  AV+ A  AK RN G+ C +  RF V + + DEF R L  
Sbjct: 262 TSMELGGNAPFLVFADADLDAAVEGAFQAKMRNVGEACTAANRFYVQSPVADEFARRLAD 321

Query: 310 HAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPT 369
               L VG+GL+  T +G L +   +  + +++ +A   GA++ TGG  + S+G+FFAPT
Sbjct: 322 RLAALPVGHGLDPDTQVGPLIDANAVKNVTALVADATSAGATVLTGGGPVPSDGHFFAPT 381

Query: 370 VIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQ 429
           V+  VPL A     E FGPVA I  FD  + A+A AN   +GLAGY FT S +    +++
Sbjct: 382 VLEGVPLGARTLAEEIFGPVAPIVAFDDEDTAVALANDSEYGLAGYLFTESLSRGLRVSE 441

Query: 430 RLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTVMA 480
           RLE GM+ +NQ     P  PFGGVK SG G EGG   ++ YL  K + + A
Sbjct: 442 RLECGMVGLNQGIISNPAAPFGGVKQSGLGREGGAVGIDEYLSVKYLAIKA 492


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: 659
Number of extensions: 27
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: 494
Length adjustment: 34
Effective length of query: 447
Effective length of database: 460
Effective search space:   205620
Effective search space used:   205620
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