GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Escherichia coli BW25113

Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate 15537 b1415 aldehyde dehydrogenase A, NAD-linked (NCBI)

Query= SwissProt::Q64057
         (539 letters)



>FitnessBrowser__Keio:15537
          Length = 479

 Score =  205 bits (522), Expect = 3e-57
 Identities = 139/450 (30%), Positives = 223/450 (49%), Gaps = 9/450 (2%)

Query: 71  PANNEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPKRGEIVRKIGDALREKIQLLGR 130
           PA    I+R+     +D  + I  A++A   W  +PA +R   +RKI   +RE+   +  
Sbjct: 29  PATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERASEISA 88

Query: 131 LVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSERPGHALMEQWNPLGLVGI 190
           L+  E GKI      EV    D  DY A  +R   G  + S+RPG  ++     LG+   
Sbjct: 89  LIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPGENILLFKRALGVTTG 148

Query: 191 ITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVTKIIAKVLEDNLLPGAICSL 250
           I  +NFP  +     A AL+TGN  + K +  T   +IA     AK++++  LP  + +L
Sbjct: 149 ILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIA----FAKIVDEIGLPRGVFNL 204

Query: 251 TCG-GADMGTAMARDERVNLLSFTGSTQVGKQVALMVQERFGKSLLELGGNNAIIAFEDA 309
             G G  +G  +A + +V ++S TGS   G+++     +   K  LELGG    I  +DA
Sbjct: 205 VLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVMDDA 264

Query: 310 DLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDRLKNAYSQIRVGNPWDPN-IL 368
           DL L + + + + V  +GQ C    R+++ + I+D+ V+RL  A   ++ GNP + N I 
Sbjct: 265 DLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERNDIA 324

Query: 369 YGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMDHPGNYVEPTIVTGLVHDAPIVHKET 428
            GPL    A+    Q V  A +EG  V +GGK ++  G Y  PT++  +  +  I+H+ET
Sbjct: 325 MGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMHEET 384

Query: 429 FAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCGIVNVNIPTS 488
           F P+L V  F   E+     N+   GL+SSI+T++L    + +  KG   G   +N    
Sbjct: 385 FGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAI--KGLKFGETYINRENF 442

Query: 489 GAEIGGAFGGEKHTGGGRESGSDAWKQYMR 518
            A + G   G + +G G   G     +Y++
Sbjct: 443 EA-MQGFHAGWRKSGIGGADGKHGLHEYLQ 471


Lambda     K      H
   0.319    0.137    0.417 

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: 641
Number of extensions: 31
Number of successful extensions: 3
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: 539
Length of database: 479
Length adjustment: 34
Effective length of query: 505
Effective length of database: 445
Effective search space:   224725
Effective search space used:   224725
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