GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Shewanella sp. ANA-3

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate 7023012 Shewana3_0250 aldehyde dehydrogenase (RefSeq)

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



>FitnessBrowser__ANA3:7023012
          Length = 506

 Score =  338 bits (867), Expect = 3e-97
 Identities = 195/475 (41%), Positives = 282/475 (59%), Gaps = 15/475 (3%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           FI  ++V   +   F   SP   +   ++  +   DI+ A++AA AA   +W  +    R
Sbjct: 22  FIGGKWVAPVNGDYFENRSPVNGQNFCKIPRSDYRDIELALDAAHAA-KDAWGKTSVTER 80

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGSVI 142
             +L ++AD ++++ + LA  E  +NGK++  +   D+ L   +FR  AG     +GS  
Sbjct: 81  ANLLLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEGSAA 140

Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202
           +      +Y   EP+GV GQIIPWNFPLLMA+WK+ P L  G   VLK AE TP+S L L
Sbjct: 141 DIDGNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPVSILVL 200

Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262
             LI++   PPG++NVV+GFG  AG  +++  +I K+AFTGST  G HI+K AAES +  
Sbjct: 201 LELIEDL-LPPGILNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGYHILKCAAESLIPS 259

Query: 263 VTLELGGKSPNIVFDDA--DVKSTIQHLVTGI---FYNTGEVCCAGSRIYVQEGIYDKIV 317
            T+ELGGKSPN+ F D        +   V G+   F+N GEVC   SR+ +QE IYD+ +
Sbjct: 260 -TVELGGKSPNLYFADVMDHEDEYLDKAVEGMLLAFFNQGEVCTCPSRVLIQESIYDRFI 318

Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG-----ERF 372
            +    A+++K G+P    T +GAQ SQ Q DKIL Y+ IGK EGA V+ GG     E  
Sbjct: 319 EKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGKDEGAQVLLGGSLCQLEGD 378

Query: 373 GNKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTT 432
            +KGY+I PTI     +  +I ++EIFGPV+++T FK   E +A+AND+EYGL AGV T 
Sbjct: 379 QSKGYYISPTIMKGHNK-MRIFQEEIFGPVISVTTFKDEAEALAIANDTEYGLGAGVWTR 437

Query: 433 NLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVK 487
           +++ A  +   I +G +W+N Y+ +     FGGY +SGIGRE  +  L++Y   K
Sbjct: 438 DMNRAQRLGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLNHYQNTK 492


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: 580
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: 495
Length of database: 506
Length adjustment: 34
Effective length of query: 461
Effective length of database: 472
Effective search space:   217592
Effective search space used:   217592
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