GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dino:3608018 Dshi_1425 aldehyde dehydrogenase
           (RefSeq)
          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 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, 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