GapMind for catabolism of small carbon sources

 

Alignments 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 202599 SO3496 aldehyde dehydrogenase (NCBI ptt file)

Query= SwissProt::O50174
         (487 letters)



>FitnessBrowser__MR1:202599
          Length = 498

 Score =  189 bits (480), Expect = 2e-52
 Identities = 147/470 (31%), Positives = 229/470 (48%), Gaps = 20/470 (4%)

Query: 5   YIAGQWL-AGQGETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPA--WARRPLEQ 61
           +I G++  A  G T + + P+   ++      D    + AV  ARE F +  W++    +
Sbjct: 24  FINGEYRDASSGNTFDCISPIDGRLLAPVASCDLMDANIAVANAREVFDSGVWSKAAPVK 83

Query: 62  RIELLERFAATLKSRADELARVIGEETGKPL-WESATEVTSMVNKVAISVQAFRERTGEK 120
           R +++ RFA  L+  A+ELA +   + GKP+ +  A +V      +  S +A  +   E 
Sbjct: 84  RKQVMIRFAELLEENANELALLETLDMGKPIRFSKAVDVAGAARAIRWSGEAIDKLYDEL 143

Query: 121 SGPLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAEL 180
           +    +   ++  +P GVVA   P+NFP  +    + PAL+ GN V+ KPSE +P  A  
Sbjct: 144 APTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALVTGNSVILKPSEKSPLTAIR 203

Query: 181 TLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQK 239
             +  +QAG+P GVLN++ G G   G ALA H  +D L FTGS++    L    G    K
Sbjct: 204 IAELAVQAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGESNMK 263

Query: 240 ILALEMGGNNP-LVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLAR 298
            + LE GG +P +V  +  DL AA     ++   + G+ CT   RLLV  G   D L+  
Sbjct: 264 RVWLEAGGKSPNIVFNDAPDLKAAAVAAAEAIGFNQGEVCTAGSRLLVESGV-KDELVGL 322

Query: 299 LVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLL---KAQEH---LIGKGAQPLLAMTQP 352
           +    A+ + G    +P    GAV+     + +L   KA ++    +  G Q +LA T  
Sbjct: 323 IAEELASWQPGH-PLEPTTVSGAVVDKQQLDTILSYIKAGQNEGASLVYGGQQVLAET-- 379

Query: 353 IDGAALLTPGIL-DVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSD 411
             G   + P +  +V    +   EE FGP+L VI ++    AI  AN T YGLAAG+ + 
Sbjct: 380 --GGVYVQPTVFSNVKNQMKIASEEIFGPVLSVIEFNGMEEAIAIANDTIYGLAAGVWTA 437

Query: 412 SRERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYAAD 461
              +  +     R+G+V W     G   +APFGG   SGN R  + ++ D
Sbjct: 438 DISKAHKTAKALRSGMV-WINHYDGGDMTAPFGGYKQSGNGRDKSLHSFD 486


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: 597
Number of extensions: 32
Number of successful extensions: 7
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: 498
Length adjustment: 34
Effective length of query: 453
Effective length of database: 464
Effective search space:   210192
Effective search space used:   210192
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 (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