GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Sinorhizobium fredii NGR234

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_012709840.1 NGR_RS27930 NADP-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>NCBI__GCF_000018545.1:WP_012709840.1
          Length = 484

 Score =  338 bits (866), Expect = 3e-97
 Identities = 188/465 (40%), Positives = 259/465 (55%)

Query: 12  LIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERA 71
           L+   W++A     I+V NPATG+ IGRV   G A+   A+  A    + W    A ERA
Sbjct: 14  LVGENWIEADPQNAIEVNNPATGEIIGRVPKLGAAETKVAIETAARVQKEWAGRTAKERA 73

Query: 72  ATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPP 131
           A +R+   L+ E  D + Q++T EQGKPL EA  E++  A  IEWFA+EGRRVYG +VP 
Sbjct: 74  AILRRWYELMIENKDDLGQILTIEQGKPLAEATGEIVYGASFIEWFAEEGRRVYGDLVPG 133

Query: 132 RNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALL 191
                +  V+K+P+G VAA TPWNFP   + RK   A A GC+ ++K   +TP S  A+ 
Sbjct: 134 HQKDKRILVMKQPIGVVAAITPWNFPNAMITRKAGPAFAAGCAMVLKPAAQTPYSAIAIA 193

Query: 192 RAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRAT 251
                AG+P G+  ++ G   EI + +  +P +RK+TFTGST VG +L   +   +K+  
Sbjct: 194 VLAERAGMPKGLFSVITGSAREIGAEMTSNPTVRKLTFTGSTEVGAELYRQSAATIKKLG 253

Query: 252 MELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHA 311
           +ELGG+AP IV +DAD+  AV+ A  AKFRN GQ C+   R  V   + D F+  L    
Sbjct: 254 LELGGNAPFIVFDDADLDAAVEGALIAKFRNNGQTCVCANRLYVQEGVYDAFSEKLAAAV 313

Query: 312 EGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVI 371
             LK GNG+E+GT LG L +   L  +   + +A   GA +  GG R    G+FF  TV+
Sbjct: 314 AKLKTGNGMEDGTILGPLIDKPALEKVEEHVADALAKGARVIQGGRRHALGGSFFEATVL 373

Query: 372 ANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRL 431
           A+V     V   E FGPVA +  F    + I +AN   FGLA Y + +  A V  + + L
Sbjct: 374 ADVTQAMAVAREETFGPVAPLFRFKDEADVIRQANDTEFGLASYFYAKDLARVFRVAEAL 433

Query: 432 EVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476
           E GM+ +N       E PFGGVK SG G EG    +E ++  K V
Sbjct: 434 EYGMVGVNTGLISTAEAPFGGVKFSGLGREGSKYGIEEFMEIKYV 478


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: 631
Number of extensions: 30
Number of successful extensions: 1
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: 484
Length adjustment: 34
Effective length of query: 447
Effective length of database: 450
Effective search space:   201150
Effective search space used:   201150
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 Apr 09 2024. 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