GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:17649
          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:

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