GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Escherichia coli BW25113

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate 17649 b3588 aldehyde dehydrogenase B (lactaldehyde dehydrogenase) (VIMSS)

Query= metacyc::MONOMER-16244
         (495 letters)



>FitnessBrowser__Keio:17649
          Length = 512

 Score =  345 bits (884), Expect = 3e-99
 Identities = 204/484 (42%), Positives = 281/484 (58%), Gaps = 19/484 (3%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           FI  E+V     + +  ++P T + + +V  +   DID A++AA       W+ +  Q R
Sbjct: 28  FIGGEWVAPADGEYYQNLTPVTGQLLCEVASSGKRDIDLALDAAHKV-KDKWAHTSVQDR 86

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVALTAAYFRSCAGWTDKIKGSVI 142
             +L+K+AD ++++ + LA  E  DNGK +   S  DV L   +FR  A      +G + 
Sbjct: 87  AAILFKIADRMEQNLELLATAETWDNGKPIRETSAADVPLAIDHFRYFASCIRAQEGGIS 146

Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202
           E       Y   EP+GV GQIIPWNFPLLMASWK+ P L  G   VLK A  TPLS L L
Sbjct: 147 EVDSETVAYHFHEPLGVVGQIIPWNFPLLMASWKMAPALAAGNCVVLKPARLTPLSVLLL 206

Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262
             ++ +   PPGVVNVV+G G   G  +++  +I KVAFTGST  G+ IM+ A + N+  
Sbjct: 207 MEIVGDL-LPPGVVNVVNGAGGVIGEYLATSKRIAKVAFTGSTEVGQQIMQYATQ-NIIP 264

Query: 263 VTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316
           VTLELGGKSPNI F      +DA     ++      F N GEVC   SR  VQE IY++ 
Sbjct: 265 VTLELGGKSPNIFFADVMDEEDAFFDKALEGFALFAF-NQGEVCTCPSRALVQESIYERF 323

Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG--- 373
           +       ES++ G+P    T MGAQ S  QL+ IL YIDIGKKEGA V+TGG R     
Sbjct: 324 MERAIRRVESIRSGNPLDSVTQMGAQVSHGQLETILNYIDIGKKEGADVLTGGRRKLLEG 383

Query: 374 --NKGYFIKPTI-FGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVH 430
               GY+++PTI FG  + + ++ ++EIFGPV+ +T FKT+EE + LAND++YGL AGV 
Sbjct: 384 ELKDGYYLEPTILFG--QNNMRVFQEEIFGPVLAVTTFKTMEEALELANDTQYGLGAGVW 441

Query: 431 TTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVR 490
           + N + A  +   I +G +W N Y+ +     FGGY QSGIGRE  +  L++Y Q K + 
Sbjct: 442 SRNGNLAYKMGRGIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLEHYQQTKCLL 501

Query: 491 IGLS 494
           +  S
Sbjct: 502 VSYS 505


Lambda     K      H
   0.316    0.133    0.389 

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: 599
Number of extensions: 22
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: 495
Length of database: 512
Length adjustment: 34
Effective length of query: 461
Effective length of database: 478
Effective search space:   220358
Effective search space used:   220358
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