GapMind for catabolism of small carbon sources

 

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

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 200843 SO1678 methylmalonate-semialdehyde dehydrogenase (NCBI ptt file)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_805
         (497 letters)



>lcl|FitnessBrowser__MR1:200843 SO1678 methylmalonate-semialdehyde
           dehydrogenase (NCBI ptt file)
          Length = 499

 Score =  199 bits (507), Expect = 1e-55
 Identities = 155/496 (31%), Positives = 234/496 (47%), Gaps = 42/496 (8%)

Query: 23  YINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQRAVENARATFNSGVWSRLAPTK 82
           YI+GE+T           +P +   +  I S  A +   A+ +A+A F +  W  +  ++
Sbjct: 8   YIDGEFTAGTGTSQIVVTNPANNATIAVINSATADEVHAAIASAKAAFKT--WKEVPVSE 65

Query: 83  RKSTMIRFAGLLKQHAEELALLETLDMGKPISDS---LYIDVPGAAQALSWS----GEAI 135
           R   M+R+  LLK+H +ELA +   + GK   D+   ++  +  A  A + +    GE +
Sbjct: 66  RARVMLRYQHLLKEHHDELATILAHETGKTFEDAKGDVWRGIEVAEHACNIASLLMGETV 125

Query: 136 DKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEK 195
           + +   +    + Q       P+GV   I P+NFP M+  W    A++ GN+ ILKPSE+
Sbjct: 126 ENVARSIDTYSYTQ-------PLGVCAGITPFNFPAMIPLWMFPLAIACGNTFILKPSEQ 178

Query: 196 SPLTAIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIY 255
            P+T  R+ EL VEAG PKGVL ++ G   T    L     V  + F GS  +  Q +  
Sbjct: 179 DPMTPQRLVELFVEAGAPKGVLQLIHG-DKTAVDILLADPAVKAISFVGSVAVG-QYIYK 236

Query: 256 SGESNMKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGEVCTAGSRLLVERSIK 315
           +G  N+KRV   AG K+  ++  DA N Q       GA     G+ C A S  +   + K
Sbjct: 237 TGTDNLKRVQAFAGAKNHCVIMPDA-NKQQVINNLVGASVGAAGQRCMAISVAVFVGAAK 295

Query: 316 DKFLPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHADGARLVAGGK--R 373
           + ++P + EAL   +PG   D     G L+       VL  I  G  +GA+ +  G    
Sbjct: 296 E-WIPELKEALAKVRPGLWDDKDAGYGPLISPAAKVRVLKLIAQGKEEGAQCLLDGSDFT 354

Query: 374 TLQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTPYGLAAAV 433
                 G +V PT+F  V+  M I +EEIFGPVL  +E DS E+AI + N +PYG   ++
Sbjct: 355 VAGFESGNWVGPTMFTKVTTDMSIYKEEIFGPVLCCMESDSLEDAIELVNASPYGNGTSI 414

Query: 434 WTADISKAHLTARALRAGSVWVNQYDGGDMTAP-----FGGFKQSGNGRDKSLHAFDK-- 486
           +TA  + A      +  G V +N      +  P     F G+K S  G     HA+ K  
Sbjct: 415 FTASGAAARKYQHEIEVGQVGINV----PIPVPLPFFSFTGWKGSFYG---DQHAYGKQA 467

Query: 487 ---YTELK---ATWIK 496
              YTE K   A W +
Sbjct: 468 VRFYTETKTITARWFE 483


Lambda     K      H
   0.316    0.132    0.390 

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: 580
Number of extensions: 30
Number of successful extensions: 6
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: 497
Length of database: 499
Length adjustment: 34
Effective length of query: 463
Effective length of database: 465
Effective search space:   215295
Effective search space used:   215295
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: 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