GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__MR1:200843
          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 (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