GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Shewanella oneidensis MR-1

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 203555 SO4480 aldehyde dehydrogenase (NCBI ptt file)

Query= reanno::pseudo1_N1B4:Pf1N1B4_1109
         (481 letters)



>FitnessBrowser__MR1:203555
          Length = 506

 Score =  267 bits (683), Expect = 5e-76
 Identities = 170/466 (36%), Positives = 246/466 (52%), Gaps = 16/466 (3%)

Query: 5   KRYDNYINGEWVSGADYSANINPSELT-DTIGDYAKADLAQVHAAIDAARAAFPAWSTSG 63
           ++Y N+I G+WV+  +     N S +         ++D   +  A+DAA AA  AW  + 
Sbjct: 17  EKYANFIGGKWVAPVNGKYFDNRSPVNGQNFCKIPRSDAQDIELALDAAHAAKDAWGKTS 76

Query: 64  IQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIG-EVTRAGNIFKFFAGECLRLS 122
           +  R + L ++   +    E L      E GK + E +  ++    + F++FAG C+R  
Sbjct: 77  VTERSNILLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAG-CIRAQ 135

Query: 123 GDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPG 182
                 +          E LGVVG I PWNFP+ + AWKIAPALA GNCVVLKPA+  P 
Sbjct: 136 EGSAADIDGNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPV 195

Query: 183 CAWALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVS 242
               L E+I     P GV N+V G G   G AL  S ++  ++FTGS  VG  I      
Sbjct: 196 SILVLLELIEDL-LPPGVLNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGFHILKCAAE 254

Query: 243 RQAKVQLEMGGKNPQI----ILDDAD--LKQAVELSVQSAFYSTGQRCTASSRFIVTAGI 296
                 +E+GGK+P +    ++D  D  L +AVE  +  AF++ G+ CT  SR ++   I
Sbjct: 255 SLIPSTVELGGKSPNLYFADVMDQEDEYLDKAVE-GMLLAFFNQGEVCTCPSRVLIQESI 313

Query: 297 HDKFVEAMAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLV 356
           +D+F+E +  R ++IK G+ L T T +G   SQ Q ++ L Y+ IG+ EGA+++ GG L 
Sbjct: 314 YDRFIEKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGKDEGAQVLLGGSLC 373

Query: 357 ACDTE---GYFLAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSA 413
             + E   GY+++PT+       MRI +EEIFGPV ++    D   ALA+ANDTE+GL A
Sbjct: 374 QLEGEQSKGYYISPTIMKGHN-KMRIFQEEIFGPVISVTTFKDEAEALAIANDTEYGLGA 432

Query: 414 GIATTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYG 459
           G+ T  +  A    R  QAG V +N   A    H  FGG K S  G
Sbjct: 433 GVWTRDMNRAQRMGRGIQAGRVWINCYHA-YPAHAAFGGYKKSGIG 477


Lambda     K      H
   0.318    0.134    0.391 

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: 524
Number of extensions: 27
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: 481
Length of database: 506
Length adjustment: 34
Effective length of query: 447
Effective length of database: 472
Effective search space:   210984
Effective search space used:   210984
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