GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Escherichia coli BW25113

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 17649 b3588 aldehyde dehydrogenase B (lactaldehyde dehydrogenase) (VIMSS)

Query= BRENDA::Q8VWZ1
         (503 letters)



>FitnessBrowser__Keio:17649
          Length = 512

 Score =  332 bits (850), Expect = 3e-95
 Identities = 199/498 (39%), Positives = 287/498 (57%), Gaps = 24/498 (4%)

Query: 11  FIDGEWRVPILNKRIPNINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSAAS 70
           FI GEW  P   +   N+ P T  ++ ++ ++ K D+DLA+DAA +   +     W+  S
Sbjct: 28  FIGGEWVAPADGEYYQNLTPVTGQLLCEVASSGKRDIDLALDAAHKVKDK-----WAHTS 82

Query: 71  GSLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEE-ALADLDDVVACFEYYAGLAEELD 129
              RA  L  IA ++++  + L   E+ D GKP+ E + AD+   +  F Y+A       
Sbjct: 83  VQDRAAILFKIADRMEQNLELLATAETWDNGKPIRETSAADVPLAIDHFRYFASCIRA-- 140

Query: 130 SKQKAPISLPMDTFKSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSEL 189
             Q+  IS       +Y   EP+GVV  I PWN+P LMA+WK+APALAAG   +LKP+ L
Sbjct: 141 --QEGGISEVDSETVAYHFHEPLGVVGQIIPWNFPLLMASWKMAPALAAGNCVVLKPARL 198

Query: 190 ASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTT 249
             ++ L L EI  ++ LP GV+N+V G G   G  LA+   + K++FTGS+  G +IM  
Sbjct: 199 TPLSVLLLMEIVGDL-LPPGVVNVVNGAGGVIGEYLATSKRIAKVAFTGSTEVGQQIMQY 257

Query: 250 AAQLVKPVSLELGGKSPIVVF------EDVDLDKVAEWTVFGCF-FTNGQICSATSRLIV 302
           A Q + PV+LELGGKSP + F      ED   DK  E   F  F F  G++C+  SR +V
Sbjct: 258 ATQNIIPVTLELGGKSPNIFFADVMDEEDAFFDKALEG--FALFAFNQGEVCTCPSRALV 315

Query: 303 HESIAVEFVDKLVKWAENIKISDPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTG 362
            ESI   F+++ ++  E+I+  +PL+   ++G  VS  Q + +LN I   K EGA +LTG
Sbjct: 316 QESIYERFMERAIRRVESIRSGNPLDSVTQMGAQVSHGQLETILNYIDIGKKEGADVLTG 375

Query: 363 GRRP---EHLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHY 419
           GRR      LK GY++EPTI+     +M++++EE+FGPVLAV TF T EEA+ LANDT Y
Sbjct: 376 GRRKLLEGELKDGYYLEPTILFG-QNNMRVFQEEIFGPVLAVTTFKTMEEALELANDTQY 434

Query: 420 GLGSAVMSNDLERCERLSKALQAGIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENY 479
           GLG+ V S +     ++ + +QAG VW NC       A +GG K+SG GRE  +  LE+Y
Sbjct: 435 GLGAGVWSRNGNLAYKMGRGIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLEHY 494

Query: 480 LSVKQVTRYTSDEPWGWY 497
              K +    SD+P G +
Sbjct: 495 QQTKCLLVSYSDKPLGLF 512


Lambda     K      H
   0.317    0.134    0.402 

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: 605
Number of extensions: 27
Number of successful extensions: 7
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: 503
Length of database: 512
Length adjustment: 34
Effective length of query: 469
Effective length of database: 478
Effective search space:   224182
Effective search space used:   224182
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