GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3608018
          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 (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