GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolA in Dinoroseobacter shibae DFL-12

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)

Query= reanno::WCS417:GFF2142
         (499 letters)



>lcl|FitnessBrowser__Dino:3608018 Dshi_1425 aldehyde dehydrogenase
           (RefSeq)
          Length = 484

 Score =  208 bits (529), Expect = 4e-58
 Identities = 147/489 (30%), Positives = 230/489 (47%), Gaps = 29/489 (5%)

Query: 2   TTTIEHYINDQRVSRDDRYQDVFNPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTP 61
           T    H IN   V     ++ VFNPAT E       ASR  V +A+AAA+AA  GWA   
Sbjct: 16  TGPYRHAINGALVDSAGSFE-VFNPATDEVVAHAPNASRDQVEQAIAAAKAAQPGWAALS 74

Query: 62  PIRRARVLFEYLHLLRERKDDLARIIVAEHGKV-FTDAQGEVDRGIDILEFACGIPNLLK 120
              R   +  Y   L   K +L  ++  E GK   + A  EV+  I        +  + K
Sbjct: 75  QDERGAYIAAYADALDAHKQELITLLTTEQGKPRHSMATTEVEYAI------FWVREVAK 128

Query: 121 GEHSDQVSRGMDNWTMR---QPLGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPT 177
               D+V       T++    PLGVV  +TP+NFPV++ +W     +  GNT ++KPSP 
Sbjct: 129 RRLEDEVIEDTPEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCLVTGNTMVMKPSPY 188

Query: 178 DPSASLFMAELLREAGLPKGVFNVVQGDKESVDALIEHPDVKAVSFVGSTPIAQYIYETG 237
            P  +L   E+ ++   P GV NVV G  E    L EHPD+  +SF GST   + +  + 
Sbjct: 189 TPLCTLRFGEIAQQV-FPAGVLNVVAGGNEQGAWLTEHPDIAKISFTGSTATGRKVMASS 247

Query: 238 ARNGKRVQGLGGAKNHMVVMPDADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVGDKV 297
           + N KR+    G  +  +++P  D +  +  L  AAYG++G+ C+A+    +   + D  
Sbjct: 248 SCNLKRITLELGGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVHESLYDDF 307

Query: 298 IAALTERAKHLRITDGRDLKAEMGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPTE 357
           +      A    + +G D   ++GPI ++    ++          G  + L G   +P  
Sbjct: 308 LRDFVAHAAEKTVGNGMDPNTDLGPIQNKMQYGKLKDLFADVKAQGLSVPLGGE--IPDG 365

Query: 358 PGLENGFWLGATLFDHVTEEMSIYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSCF 417
           P    G ++  T+ D+  ++  + REE FGP+L  ++ +D  E ++  N  EFG   S +
Sbjct: 366 P----GNFVPITIVDNPPKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASVW 421

Query: 418 TRDGNIAREFARRIEVGMVGINV----PISVPMAWHGFGGWKKSLFGDMHAYGTEGVRFY 473
             D + A   A R+E G V +N      I +P     FGG K+S  G  +  G EG++ +
Sbjct: 422 GPDRDTAIGVANRLEAGTVWVNEIHIHGIDIP-----FGGHKQSGMGVEN--GQEGLKEF 474

Query: 474 TKQKSIMQR 482
           T  K+ M R
Sbjct: 475 TNTKTYMFR 483


Lambda     K      H
   0.320    0.136    0.407 

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: 600
Number of extensions: 29
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: 499
Length of database: 484
Length adjustment: 34
Effective length of query: 465
Effective length of database: 450
Effective search space:   209250
Effective search space used:   209250
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 (21.8 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