GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF3251
          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 (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