GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Phaeobacter inhibens BS107

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate GFF3174 PGA1_c32250 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC

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



>FitnessBrowser__Phaeo:GFF3174
          Length = 494

 Score =  330 bits (846), Expect = 7e-95
 Identities = 189/481 (39%), Positives = 269/481 (55%), Gaps = 8/481 (1%)

Query: 15  TTYEQPTGLF---INNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAF 71
           T   QP   F   I+ + V +    T   +SP     +TQ+      D++ A+ +A AAF
Sbjct: 8   TLRAQPVPCFSHLIDGQQVAASDGATMDVLSPIDGRLLTQIARGTVRDMERAIASARAAF 67

Query: 72  HSS-WSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSL-MCSKGDVALTAAYFRS 129
               W+   P  R KVL K A+LI+  A  LA +   DNG  + M  K +    AA  R 
Sbjct: 68  EDRRWAGQPPAARKKVLMKWAELIEADALNLAVLGVRDNGTEITMALKAEPGSAAATIRY 127

Query: 130 CAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVL 189
            A   DKI G +  T         +EP+GV G IIPWNFP+++ +WKL P L  G + VL
Sbjct: 128 YAEALDKIYGEIAPTSSDVLGMVHKEPVGVVGAIIPWNFPMMIGAWKLAPALAMGNSVVL 187

Query: 190 KTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGR 249
           K +E+  LS + +  L  EAG PPGV+N V+G G   G  +     +  + FTGS  TGR
Sbjct: 188 KPSETASLSLMRMVELALEAGLPPGVLNAVTGEGAVVGEALGLSMDVDVLVFTGSGQTGR 247

Query: 250 HIMKAAAESNLKKVTLELGGKSPNIVFDDA-DVKSTIQHLVTGIFYNTGEVCCAGSRIYV 308
            +M+ AA SNLK+V LELGGKSPNIVF DA D+    +    GIF N+G+VC AGSR+ V
Sbjct: 248 RLMEYAARSNLKRVYLELGGKSPNIVFADAPDLADAAKVTAAGIFRNSGQVCVAGSRLLV 307

Query: 309 QEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITG 368
           +  I+D  V E   AA+ +++GDP + DT +GA  S+ QL + L+++   + EG  +ITG
Sbjct: 308 EASIHDAFVEEVAKAAQMMRVGDPLRLDTQIGAINSEAQLARNLQFVARAEVEGGQIITG 367

Query: 369 GERFGNK--GYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLA 426
           G+R  ++  G ++ PTI   V  D  + ++E+FGPV+ +T F+T  E + +AN + YGLA
Sbjct: 368 GQRLLSETGGSYMAPTIVTGVTPDATLAQEEVFGPVLAVTPFETDAEALRIANATVYGLA 427

Query: 427 AGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQV 486
             V T+ L+ A  +   + +G + VNTY      VP GG  QSG G +    A+D Y  +
Sbjct: 428 GAVWTSGLTRAHRMVQGVRTGVMHVNTYGGADGTVPLGGVGQSGNGADKSLHAIDKYINL 487

Query: 487 K 487
           K
Sbjct: 488 K 488


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: 511
Number of extensions: 26
Number of successful extensions: 5
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: 494
Length adjustment: 34
Effective length of query: 461
Effective length of database: 460
Effective search space:   212060
Effective search space used:   212060
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