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

GapMind for catabolism of small carbon sources

Aligments 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources