GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Shewanella oneidensis MR-1

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate 203555 SO4480 aldehyde dehydrogenase (NCBI ptt file)

Query= SwissProt::O50174
         (487 letters)



>lcl|FitnessBrowser__MR1:203555 SO4480 aldehyde dehydrogenase (NCBI
           ptt file)
          Length = 506

 Score =  151 bits (381), Expect = 6e-41
 Identities = 153/472 (32%), Positives = 228/472 (48%), Gaps = 42/472 (8%)

Query: 4   HYIAGQWLAG-QGETLESLDPV-GQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQ 61
           ++I G+W+A   G+  ++  PV GQ      R +DA  ++ A+ AA  A  AW +  + +
Sbjct: 21  NFIGGKWVAPVNGKYFDNRSPVNGQNFCKIPR-SDAQDIELALDAAHAAKDAWGKTSVTE 79

Query: 62  RIELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNK-VAISVQAFRERTG-- 118
           R  +L R A  ++   + LA     ET    WE+   V   +N  + + V  FR   G  
Sbjct: 80  RSNILLRIADRVEQNLEYLAVA---ET----WENGKAVRETLNADLPLFVDHFRYFAGCI 132

Query: 119 ---EKSGPLADATAVLRH--KPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSEL 173
              E S    D   V  H  +P GVV    P+NFP  +    I PAL AGNCVV KP+E 
Sbjct: 133 RAQEGSAADIDGNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQ 192

Query: 174 TPKVAELTLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQ 232
           TP V+ L L   I+  LP GVLN+V G G E G ALA  + +  L FTGS+  G  +  +
Sbjct: 193 TP-VSILVLLELIEDLLPPGVLNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGFHI-LK 250

Query: 233 FGGQPQKILALEMGGNNP-LVVEEVAD-----LDAAVYTIIQSAFISAGQRCTCARRLLV 286
              +      +E+GG +P L   +V D     LD AV  ++  AF + G+ CTC  R+L+
Sbjct: 251 CAAESLIPSTVELGGKSPNLYFADVMDQEDEYLDKAVEGML-LAFFNQGEVCTCPSRVLI 309

Query: 287 PQGAWGDALLARLVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHL-IGK--GA 343
            +  + D  + +++A + T++ G     P      V + ++ E   K   +L IGK  GA
Sbjct: 310 QESIY-DRFIEKVLARAQTIKQG----NPLDTATQVGAQASQEQFDKILSYLAIGKDEGA 364

Query: 344 QPLLAMTQ-PIDG----AALLTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREAN 398
           Q LL  +   ++G       ++P I+          EE FGP++ V  + D A A+  AN
Sbjct: 365 QVLLGGSLCQLEGEQSKGYYISPTIMKGHNKMRIFQEEIFGPVISVTTFKDEAEALAIAN 424

Query: 399 ATQYGLAAGLLSDSRERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASG 450
            T+YGL AG+ +    R ++     +AG V W        + A FGG   SG
Sbjct: 425 DTEYGLGAGVWTRDMNRAQRMGRGIQAGRV-WINCYHAYPAHAAFGGYKKSG 475


Lambda     K      H
   0.318    0.134    0.396 

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: 572
Number of extensions: 36
Number of successful extensions: 5
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: 487
Length of database: 506
Length adjustment: 34
Effective length of query: 453
Effective length of database: 472
Effective search space:   213816
Effective search space used:   213816
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 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