GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Sinorhizobium meliloti 1021

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate SMa1848 SMa1848 GabD5 succinate semialdehyde dehdyrogenase

Query= BRENDA::Q88RC0
         (480 letters)



>lcl|FitnessBrowser__Smeli:SMa1848 SMa1848 GabD5 succinate
           semialdehyde dehdyrogenase
          Length = 484

 Score =  566 bits (1458), Expect = e-166
 Identities = 283/476 (59%), Positives = 354/476 (74%), Gaps = 2/476 (0%)

Query: 1   MQLKDAQLFRQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKA 60
           M+LKD +LFRQ   I GEW+   +G  + V +PA   V+GTVP MGTAETR AIEAA+ A
Sbjct: 1   MRLKDRELFRQLGLIGGEWIAGASGVVVDVIDPANQAVLGTVPDMGTAETRAAIEAANAA 60

Query: 61  LPAWRALTAKERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFA 120
              W+  T  ER+A L RW  LMIEN +DLA L+T EQGKPL EA+GEI Y A+F++WFA
Sbjct: 61  FGPWKKKTHAERAAVLERWHALMIENLEDLAVLVTMEQGKPLEEARGEIRYGAAFVKWFA 120

Query: 121 EEAKRIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180
           EE++RI G TIP    D+R++V+K+ +GV A +TPWNFP AMITRK  PALAAGCT+V+K
Sbjct: 121 EESRRIGGHTIPSPTSDRRIVVLKEAVGVCAIVTPWNFPNAMITRKVAPALAAGCTVVIK 180

Query: 181 PASQTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQ 240
           P+  TP+SALAL  LA RAGIPAGV+++VTG    +G E   N  VRK+SFTGST +G  
Sbjct: 181 PSEFTPFSALALGVLAERAGIPAGVVNIVTGMPTAIGNEFMTNETVRKISFTGSTRVGSL 240

Query: 241 LMEECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDG 300
           LM   A  +K++SLELGGNAPFIVFDDA+LD AVEGAI SK+RN GQTCVCANRI VQ G
Sbjct: 241 LMRGAADSVKRLSLELGGNAPFIVFDDANLDLAVEGAIASKFRNGGQTCVCANRILVQAG 300

Query: 301 VYDAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKL 360
           VYDAFAEKL A V  +K+G G E G   GP+I+  A+ K+  H+EDA++KGAK+ + G+ 
Sbjct: 301 VYDAFAEKLGARVNAMKVGPGTEPGIAIGPMINEAAIDKIDRHVEDAIAKGAKLAARGRS 360

Query: 361 I-EG-NFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418
           + EG  +  P +L        +A EETFGP+APLFRF+ E E IA++N T FGLA+YFY 
Sbjct: 361 VPEGRQYTAPIVLTGATTDMLLASEETFGPVAPLFRFETEDEAIAIANGTPFGLAAYFYT 420

Query: 419 RDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474
             + R +RVAEALE+GM+G+NTG IS EVAPFGG+K SGLGREG++ GIE+YLE+K
Sbjct: 421 EGLKRSWRVAEALEFGMIGLNTGAISTEVAPFGGVKQSGLGREGAQVGIEEYLEMK 476


Lambda     K      H
   0.317    0.134    0.384 

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: 657
Number of extensions: 17
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: 480
Length of database: 484
Length adjustment: 34
Effective length of query: 446
Effective length of database: 450
Effective search space:   200700
Effective search space used:   200700
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 (21.6 bits)
S2: 52 (24.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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