GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Sphingomonas koreensis DSMZ 15582

Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate Ga0059261_3926 Ga0059261_3926 L-proline dehydrogenase (EC 1.5.99.8)/delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)

Query= curated2:Q12QD2
         (498 letters)



>FitnessBrowser__Korea:Ga0059261_3926
          Length = 1199

 Score =  183 bits (465), Expect = 3e-50
 Identities = 153/475 (32%), Positives = 230/475 (48%), Gaps = 34/475 (7%)

Query: 2   NQLEQLTPLTQTQFIAGQWLAGK----GPSFSSVNPANG-EVIWQGLGADAGQVDAAITS 56
           N L +L    +    AG W A      G S    NPA+G +V+   +         A+ +
Sbjct: 543 NVLAELAASLKVSAAAG-WAAEPADRIGTSRPVYNPADGKDVVGTVVEVTPEAAQTAVAT 601

Query: 57  ARAAFYTWSAMSLTERLVIVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKI 116
           A+AA   W+A++  ER   ++  A+ +++  ++    I  E GK+   +  EV     + 
Sbjct: 602 AQAAAADWAAVAPAERAACLDRAADIMQDRMQILMGLIIREAGKSAPNAIAEV-----RE 656

Query: 117 AIS-IKANAERTGTVENPMPGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNT 175
           AI  ++  AE+       M GA     HKP G V    P+NFP  +  G +  AL+AGNT
Sbjct: 657 AIDFLRYYAEQA----RAMLGAA----HKPLGAVTCISPWNFPLAIFTGQVAAALVAGNT 708

Query: 176 VLFKPSELTPKVAELTMQLWQQAGLPNGVLNLLQGEIATGKALASHKGIDGLFFTGSSNT 235
           VL KP+E TP +A   + +  +AG+P   L L+ G+   G AL +  G   + FTGS+  
Sbjct: 709 VLAKPAEETPLIAAQGVSILHEAGIPAAALQLVPGDGRIGAALVAAPGTQAVMFTGSTEV 768

Query: 236 GHLLHQQYA------GQPGKILALEMGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCT 289
             ++ ++ A      G P   +A E GG N +I+   A  +  V D+I SAF S+GQRC+
Sbjct: 769 ARIIQKELAKRLTDGGDPVPFIA-ETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCS 827

Query: 290 CARRLFIPKTANGDAILAKLLTSTAKIALGDPFAETQPFFGAMISDKAAAGMVKAQADIQ 349
             R L +      D IL  L  +  ++++G   + +    G +I+ +A A +    A + 
Sbjct: 828 ALRVLCLQDDV-ADRILVMLKGALHELSIGRTDSLSTD-IGPVITAEAKANIEGHIARML 885

Query: 350 AAG-GVSLIELTQVTPGLGFVTPGIIDVTDASPLADEEHFGPLLKVYRY--TDFDAAIDE 406
             G GV  IEL   T    FV P II++   + L + E FGP+L V RY   D D  ID 
Sbjct: 886 GMGRGVEQIELAGETAQGTFVPPTIIELQSIADL-EREVFGPVLHVVRYKRRDLDRVIDA 944

Query: 407 ANNTSFGLSAGLLADSETDYQHFYRRIRAGIVNWNKPITGA-SSAAPFGGIGASG 460
            N T +GL+ GL    +    H  +R+ AG +  N+ I GA     PFGG G SG
Sbjct: 945 INATGYGLTFGLHTRLDETIAHVSQRVEAGNLYINRNIIGAVVGVQPFGGRGLSG 999


Lambda     K      H
   0.317    0.133    0.390 

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: 1333
Number of extensions: 64
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 1
Length of query: 498
Length of database: 1199
Length adjustment: 41
Effective length of query: 457
Effective length of database: 1158
Effective search space:   529206
Effective search space used:   529206
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: 55 (25.8 bits)

This GapMind analysis is from Sep 17 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