GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Marinobacter adhaerens HP15

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate GFF3202 HP15_3144 NAD-dependent aldehyde dehydrogenase

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



>FitnessBrowser__Marino:GFF3202
          Length = 533

 Score =  360 bits (925), Expect = e-104
 Identities = 205/478 (42%), Positives = 292/478 (61%), Gaps = 17/478 (3%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           +I  E+V     + F  ++P T   I ++  + +EDID A++AA  A   +W  + P  R
Sbjct: 49  YIGGEWVAPVKGQYFENITPVTGNVICEIPRSSAEDIDLALDAAHKAA-PAWGKTSPTER 107

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGSVI 142
             +L K+AD I+ + + LA  E  DNGK++  +   D+ L A +FR  AG     +G + 
Sbjct: 108 SNILLKIADRIEANLEKLAVAETWDNGKAVRETLNADIPLAADHFRYFAGCLRAQEGHMG 167

Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202
           E       Y   EP+GV GQIIPWNFP+LMA+WKLGP L  G  TVLK AE TP S L L
Sbjct: 168 EIDHNTVAYHFHEPLGVVGQIIPWNFPILMAAWKLGPCLAAGNCTVLKPAEQTPASILVL 227

Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262
             +I +   PPGV+N+V+G+G  AG  +++  +I K+AFTGST  G HI+K AAE N+  
Sbjct: 228 MEIIGDL-LPPGVLNIVNGYGIEAGQALATSKRIAKIAFTGSTPVGSHILKCAAE-NIIP 285

Query: 263 VTLELGGKSPNIVFDDADVKST--IQHLVTGI---FYNTGEVCCAGSRIYVQEGIYDKIV 317
            T+ELGGKSPNI F D        I   V G+   F+N GEVC   SR  VQE ++++ +
Sbjct: 286 STVELGGKSPNIYFSDVMKAEPEFIDKCVEGLVLAFFNQGEVCTCPSRALVQEDMFEEFM 345

Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG---- 373
            +     +S+K G+P   D  +GAQ S+ Q DKI+ Y+ IGK+EGA V+TGG+R      
Sbjct: 346 QKVVQRTKSIKRGNPLDTDVQVGAQASKEQFDKIMSYLAIGKEEGAVVLTGGDREHLDEE 405

Query: 374 -NKGYFIKPTIF-GDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHT 431
            N G++I+PT+F GD K   ++ ++EIFGPVV +T FKT EE +A+AND+E+GL AGV T
Sbjct: 406 FNNGFYIQPTLFKGDNKM--RVFQEEIFGPVVGVTTFKTEEEALAIANDTEFGLGAGVWT 463

Query: 432 TNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489
            + + A  +   I +G +W+N Y+ +     FGGY +SG+GRE  + AL++Y Q K +
Sbjct: 464 RDTNLAYRMGRNIQAGRVWMNCYHAYPAHAAFGGYKKSGVGRETHKMALEHYQQTKCM 521


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: 690
Number of extensions: 31
Number of successful extensions: 8
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: 533
Length adjustment: 35
Effective length of query: 460
Effective length of database: 498
Effective search space:   229080
Effective search space used:   229080
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