GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Paraburkholderia bryophila 376MFSha3.1

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate H281DRAFT_01117 H281DRAFT_01117 aldehyde dehydrogenase (NAD+)

Query= reanno::SB2B:6938906
         (486 letters)



>FitnessBrowser__Burk376:H281DRAFT_01117
          Length = 795

 Score =  209 bits (531), Expect = 4e-58
 Identities = 151/456 (33%), Positives = 225/456 (49%), Gaps = 24/456 (5%)

Query: 4   FINGQWLA-GEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEGRQ 62
           FI G W A   G +  S  PA+GE +        A + AA+ AAR AQ  W  LG +GR 
Sbjct: 36  FIGGAWHAPASGAQFVSHAPASGERLADIAQGDAADIDAALAAARAAQPGWLALGGKGRA 95

Query: 63  AIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEVNE 122
             + A    ++ +    A + A + GKP  ET      ++ +  L  + + +   +E  +
Sbjct: 96  RHLYALARMVQRHSRLFAVLEALDNGKPIRETRDLDVPLVARHFLHHAGWAQLQDSEFAD 155

Query: 123 GAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELMLK 182
                    H P GV+    P+NFP  +    I PA+  GN VV KP+E TP  A L  +
Sbjct: 156 ---------HAPLGVIGQIVPWNFPLLMLAWKIAPAIATGNCVVLKPAEYTPLTALLFAE 206

Query: 183 LWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKILAL 242
           L  +AGLPAGV+N+V G+  TG AL  HPQ+D + FTGS+  G L+    AG  GK L L
Sbjct: 207 LAHQAGLPAGVLNVVTGDGSTGAALVEHPQVDKIAFTGSTEVGKLIRSVTAG-SGKSLTL 265

Query: 243 EMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVEAV 302
           E+GG +P IV   +D   A+  ++ + + + GQ C    RL V++G E  + +A L   +
Sbjct: 266 ELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVCCAGSRLLVQEGIEA-RFIAKLKRRM 324

Query: 303 KAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEM-----THLQAGTGL 357
           + ++VGP + D    MG+++        L+   +L+  G +    +     T L A    
Sbjct: 325 ETLRVGP-SLDKSIDMGAIVDPV----QLERIHSLVETGRREGCAIWQAADTPLPANGCF 379

Query: 358 VSPGLI-DVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYE 416
             P L+ +V     L  EE FGP+L  + + + DEAI LAN++RYGL+A + ++      
Sbjct: 380 YPPTLVTNVAPASTLAQEEIFGPVLVTMSFRTPDEAIALANNSRYGLAASVWSETIGRAL 439

Query: 417 YFLARIRAGIVNWNKQITGASGAAPFGGVGASGNHR 452
               R+ AG+V W         A  FGG   SG  R
Sbjct: 440 DVAPRLAAGVV-WVNATNLFDAAVGFGGYRESGYGR 474



 Score = 64.3 bits (155), Expect = 1e-14
 Identities = 52/198 (26%), Positives = 81/198 (40%), Gaps = 2/198 (1%)

Query: 39  VQAAVMAARDAQFEWFMLGFEGRQAIVEAYRNELEANKAELAEVIAQETGKPRWETATEA 98
           ++ AV AAR AQ +W       R  ++      L     E A  +    G        E 
Sbjct: 559 IRNAVQAARAAQ-KWSQASTHNRAQVLFYLAENLAVRADEFAHQLTVRNGATDAAAHAEV 617

Query: 99  AAMIGKIGLSVSAYHKRTGTEVNEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPA 158
            A + ++    +   K  G        G A+  H+P GV+ +  P   P         PA
Sbjct: 618 EASVTRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGIACPDEAPLLAFVSLAAPA 677

Query: 159 LLAGNTVVFKPSELTPKVAELMLKLWEKAGLPAGVINLVQGEVET-GKALASHPQLDGLF 217
           L  GN VV  P E  P       ++ E + +P GV+N+V G+ E    ALA H  +D ++
Sbjct: 678 LAMGNRVVVLPGEACPLAVTDFYQVVETSDVPGGVVNIVTGKREALLPALARHDDVDAVW 737

Query: 218 FTGSSRTGHLLHQQYAGH 235
             GS+    L+ ++  G+
Sbjct: 738 CFGSAADATLIERESVGN 755


Lambda     K      H
   0.317    0.133    0.393 

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: 948
Number of extensions: 57
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 486
Length of database: 795
Length adjustment: 37
Effective length of query: 449
Effective length of database: 758
Effective search space:   340342
Effective search space used:   340342
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: 53 (25.0 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