GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Dinoroseobacter shibae DFL-12

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P76217
         (492 letters)



>FitnessBrowser__Dino:3608018
          Length = 484

 Score =  183 bits (465), Expect = 1e-50
 Identities = 144/447 (32%), Positives = 212/447 (47%), Gaps = 10/447 (2%)

Query: 5   INGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAV 64
           ING  +   G+  V  NP + EV+    +A   QVEQA  AA+AA P WA LS  ER A 
Sbjct: 23  INGALVDSAGSFEVF-NPATDEVVAHAPNASRDQVEQAIAAAKAAQPGWAALSQDERGAY 81

Query: 65  VERFAALLESNKAELTAIIARETGKPRWE-AATEVTAMINKIAISIKAYHVRTGEQRSEM 123
           +  +A  L+++K EL  ++  E GKPR   A TEV   I    +   A      E   + 
Sbjct: 82  IAAYADALDAHKQELITLLTTEQGKPRHSMATTEVEYAI--FWVREVAKRRLEDEVIEDT 139

Query: 124 PDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMRL 183
           P+    + H P GV+    P+NFP  L    I P L+ GNT++ KPS  TP        +
Sbjct: 140 PEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCLVTGNTMVMKPSPYTPLCTLRFGEI 199

Query: 184 WQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILALE 243
            QQ   P GVLN+V GG E G  L+   D+  + FTGS  TG ++    S   ++I  LE
Sbjct: 200 AQQV-FPAGVLNVVAGGNEQGAWLTEHPDIAKISFTGSTATGRKVMASSSCNLKRI-TLE 257

Query: 244 MGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQ 303
           +GGN+P I+    D    +     +A+  +GQ C   +RL +      D FL   VA + 
Sbjct: 258 LGGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVHESLYDD-FLRDFVAHAA 316

Query: 304 RLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPGII 363
             T GN  D P   +G + ++    ++   +  ++A G    L   +     + +   I+
Sbjct: 317 EKTVGNGMD-PNTDLGPIQNKMQYGKLKDLFADVKAQGLSVPLGGEIPDGPGNFVPITIV 375

Query: 364 EMTGV-AGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEA 422
           +     + V  EE FGP+L + ++   DE +R AN+T FGL+  +  P+R+    +    
Sbjct: 376 DNPPKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASVWGPDRDTAIGVANRL 435

Query: 423 RAGIVNWNKPLTGAASTAPFGGIGASG 449
            AG V W   +       PFGG   SG
Sbjct: 436 EAGTV-WVNEIHIHGIDIPFGGHKQSG 461


Lambda     K      H
   0.318    0.134    0.412 

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: 611
Number of extensions: 30
Number of successful extensions: 4
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: 492
Length of database: 484
Length adjustment: 34
Effective length of query: 458
Effective length of database: 450
Effective search space:   206100
Effective search space used:   206100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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