GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Phaeobacter inhibens BS107

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate GFF1905 PGA1_c19350 putative aldehyde dehydrogenase

Query= CharProtDB::CH_018413
         (862 letters)



>FitnessBrowser__Phaeo:GFF1905
          Length = 469

 Score =  246 bits (628), Expect = 2e-69
 Identities = 141/397 (35%), Positives = 222/397 (55%), Gaps = 7/397 (1%)

Query: 49  LAKAAVLETGMGLVEDKVIKNHFAGEYIYNKYKDEKTCGIIERNEPYGITKIAEPIGVVA 108
           LA+  V E+G+G    +  K  F  + +        + G++E +E  G+ K A+P GV+A
Sbjct: 55  LAEKGVDESGIGDRAGRPAKR-FKIQMVLRDVLRTPSTGVVEVDEEKGLVKYAKPAGVIA 113

Query: 109 AIIPVTNPTSTTIFKSLISLKTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIG 168
           ++IP+TNP  T     + S   RN + FSPHPR   +T    + +  A V  GAP ++  
Sbjct: 114 SLIPMTNPAMTPPVTGVSSANARNAVIFSPHPRTAGTTFDMTEMMRKACVAVGAPADLFQ 173

Query: 169 WIDEPSIELTQYLMQKADITLATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMA 228
            +  PSI LTQ+LM++ D+TLATGG  +VK+AYSSG+PA GVG GN+ ++IDE+A I +A
Sbjct: 174 AVRHPSIPLTQHLMEECDLTLATGGKPMVKAAYSSGRPAYGVGAGNSSIVIDETADIDIA 233

Query: 229 VSSIILSKTYDNGVICASEQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIFKD- 287
             +  +SKT D G  C+++ ++I+ +S+Y+ +    +  G Y+    E   + + ++ + 
Sbjct: 234 AQNTRISKTSDFGSGCSADGNIIIQRSVYDDMVKALEAEGGYLCSPAEKTLLEKAMWDEK 293

Query: 288 GSVNPKIVGQSAYTIAAMAGIKVPKTTRILIGEVTS-LGEEEPFAHEKLSPVLAMYEADN 346
           G+     +       A +AG  +P   + L+ E  S +G E  F+ EKL+ V+A+Y  + 
Sbjct: 294 GNRTFTTIACKPQQTADVAGFSIPDDRKFLMVENQSQIGPEHKFSKEKLTTVMALYHFET 353

Query: 347 FDDALKKAVTLINLGGLGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDL 406
           FDDAL+    +   GG+GH+ GIY+      D ID  +      R  V  P S+  +G  
Sbjct: 354 FDDALETVRQIYATGGVGHSCGIYSHN---DDNIDALARVAPVSRMMVRQPQSKANAGSW 410

Query: 407 YNFRIPPSFTLGCGFWGGNSVSENVGPKHLLNIKTVA 443
            N  +P + +LGCG WGGN  +ENV  KH++N   VA
Sbjct: 411 TN-GMPMTSSLGCGIWGGNITNENVTMKHMMNYTWVA 446


Lambda     K      H
   0.317    0.134    0.378 

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: 847
Number of extensions: 29
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: 862
Length of database: 469
Length adjustment: 38
Effective length of query: 824
Effective length of database: 431
Effective search space:   355144
Effective search space used:   355144
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: 54 (25.4 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