GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Phaeobacter inhibens BS107

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate GFF3251 PGA1_c33040 aldehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



>lcl|FitnessBrowser__Phaeo:GFF3251 PGA1_c33040 aldehyde
           dehydrogenase
          Length = 479

 Score =  324 bits (831), Expect = 4e-93
 Identities = 178/472 (37%), Positives = 272/472 (57%), Gaps = 11/472 (2%)

Query: 10  RQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTA 69
           ++  +I+G WV        +V +P+T      +    AA+T  A+ AA  ALP W     
Sbjct: 4   KRDFYINGQWVAPAAPNDFEVIDPSTEAPCAVISLGDAADTNAAVAAAKTALPGWMTTPV 63

Query: 70  KERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASF-IEWFAEEAKRIYG 128
           +ER   + +  E+     +DLA+ M++E G P+  A+ +   A S+ +  F + AK    
Sbjct: 64  EERIALVEKLIEVYESRTEDLAQAMSVEMGAPIDMARTQQAGAGSWHLRNFIKAAKAFSF 123

Query: 129 DVIPG-HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPF 187
           D   G H P+ R  +I + +GV A ITPWN+P   +T K G A  AGCTMVLKP+ Q+P 
Sbjct: 124 DAPLGDHAPNDR--IIHEAVGVAALITPWNWPMNQVTLKVGAAAIAGCTMVLKPSEQSPL 181

Query: 188 SAFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAK 247
           +A   AE+   AG PAGVF++V+G    +G++L+S+P V  +SFTGST  G  +    A 
Sbjct: 182 NAMIFAEMMDEAGFPAGVFNLVNGDGTGVGTQLSSHPDVDMVSFTGSTRAGTAISKAAAD 241

Query: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAE 307
            +KKV LELGG    ++FDDAD +KAV+  ++    N GQ+C   +R+ +Q G+YD   E
Sbjct: 242 TLKKVHLELGGKGANVIFDDAD-EKAVKRGVLHMMNNTGQSCNAPSRMLVQKGIYDKAVE 300

Query: 308 KLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAG--GKP---ME 362
           +      K+++G     G   GP+++E    K+Q+ I   + +GA ++AG  G+P    +
Sbjct: 301 EAAAVANKVEVGPASSEGRHIGPVVNELQWGKIQDLIQKGIDEGARLVAGGTGRPDGLNQ 360

Query: 363 GNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLG 422
           G + +PT+  +V N   +A+EE FGP+  +  F+ E D I ++NDT +GL +Y   +DL 
Sbjct: 361 GFYVKPTVFADVNNQMTIAREEIFGPVLSIIPFESEEDAIEIANDTPYGLTNYVQTQDLA 420

Query: 423 RVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474
           R  R+A  L  GM+ +N G   +  +PFGG+K SG GREG  +GIED+LE+K
Sbjct: 421 RANRMARKLRAGMIEMN-GKSRSAGSPFGGMKQSGNGREGGSWGIEDFLEVK 471


Lambda     K      H
   0.317    0.135    0.390 

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: 583
Number of extensions: 24
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: 480
Length of database: 479
Length adjustment: 34
Effective length of query: 446
Effective length of database: 445
Effective search space:   198470
Effective search space used:   198470
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 (21.7 bits)
S2: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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