GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Escherichia coli BW25113

Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate 17649 b3588 aldehyde dehydrogenase B (lactaldehyde dehydrogenase) (VIMSS)

Query= SwissProt::A1B4L2
         (508 letters)



>lcl|FitnessBrowser__Keio:17649 b3588 aldehyde dehydrogenase B
           (lactaldehyde dehydrogenase) (VIMSS)
          Length = 512

 Score =  741 bits (1914), Expect = 0.0
 Identities = 356/507 (70%), Positives = 416/507 (82%)

Query: 2   PNDQTHPFRGVNALPFEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIE 61
           P+ Q  P      L  + RYDNFIGGEWVAP  G Y+ N TP+TG  + ++A S   DI+
Sbjct: 6   PSAQIKPGEYGFPLKLKARYDNFIGGEWVAPADGEYYQNLTPVTGQLLCEVASSGKRDID 65

Query: 62  LALDAAHAAKEKWGATSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLP 121
           LALDAAH  K+KW  TS  +RA I+ KIADRME+NLELLATAETWDNGKPIRET AAD+P
Sbjct: 66  LALDAAHKVKDKWAHTSVQDRAAILFKIADRMEQNLELLATAETWDNGKPIRETSAADVP 125

Query: 122 LAIDHFRYFAGVLRAQEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAI 181
           LAIDHFRYFA  +RAQEG IS++D +TVAYHFHEPLGVVGQIIPWNFPLLMA WK+APA+
Sbjct: 126 LAIDHFRYFASCIRAQEGGISEVDSETVAYHFHEPLGVVGQIIPWNFPLLMASWKMAPAL 185

Query: 182 AAGNCVVLKPAEQTPAGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFT 241
           AAGNCVVLKPA  TP  +++   ++GDLLPPGV+N+VNG G   G+ LA+S RIAK+AFT
Sbjct: 186 AAGNCVVLKPARLTPLSVLLLMEIVGDLLPPGVVNVVNGAGGVIGEYLATSKRIAKVAFT 245

Query: 242 GETTTGRLIMQYASENLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGE 301
           G T  G+ IMQYA++N+IPVTLELGGKSPNIFFADV  E+D FFDKALEGF +FA NQGE
Sbjct: 246 GSTEVGQQIMQYATQNIIPVTLELGGKSPNIFFADVMDEEDAFFDKALEGFALFAFNQGE 305

Query: 302 VCTCPSRVLIQESIYDKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIG 361
           VCTCPSR L+QESIY++FMERA++RV++I+ G+P +S T +GAQ S  Q E IL+Y+DIG
Sbjct: 306 VCTCPSRALVQESIYERFMERAIRRVESIRSGNPLDSVTQMGAQVSHGQLETILNYIDIG 365

Query: 362 KKEGAEVLTGGKAADLGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEA 421
           KKEGA+VLTGG+   L GEL  GYY+EPTI  G N MR+FQEEIFGPV++VTTFK   EA
Sbjct: 366 KKEGADVLTGGRRKLLEGELKDGYYLEPTILFGQNNMRVFQEEIFGPVLAVTTFKTMEEA 425

Query: 422 LEIANDTLYGLGAGVWSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRE 481
           LE+ANDT YGLGAGVWSR+ N  Y+MGRGI+AGRVWTNCYHAYPAHAAFGGYKQSGIGRE
Sbjct: 426 LELANDTQYGLGAGVWSRNGNLAYKMGRGIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRE 485

Query: 482 THKMMLDHYQQTKNMLVSYSPKKLGFF 508
           THKMML+HYQQTK +LVSYS K LG F
Sbjct: 486 THKMMLEHYQQTKCLLVSYSDKPLGLF 512


Lambda     K      H
   0.319    0.136    0.411 

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: 870
Number of extensions: 21
Number of successful extensions: 1
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: 508
Length of database: 512
Length adjustment: 34
Effective length of query: 474
Effective length of database: 478
Effective search space:   226572
Effective search space used:   226572
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 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