GapMind for catabolism of small carbon sources

 

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

Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)

Query= metacyc::MONOMER-13349
         (490 letters)



>FitnessBrowser__Dino:3607686
          Length = 506

 Score =  343 bits (879), Expect = 1e-98
 Identities = 195/488 (39%), Positives = 275/488 (56%), Gaps = 17/488 (3%)

Query: 3   QYRNYINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTT 60
           +Y N+I G++V     R FD+V P+ G VV Q+  +    V+ A+ A HAA + AWG+T+
Sbjct: 18  RYDNFIGGKFVPPVEGRYFDNVTPITGEVVGQIARSSAADVELALDAAHAA-KDAWGKTS 76

Query: 61  VAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAP 120
           V ERA I+ +IAD I+   D    AE  D GKP+   +  DIP    +FR FA +L+   
Sbjct: 77  VTERANIVLKIADRIEENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLRGQE 136

Query: 121 LDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEE 180
               + D    A    Y   +PLGVVG I PWN  +L+  WK+APA+A GN +V KP+E+
Sbjct: 137 GSMSEIDNDTVA----YHFHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQ 192

Query: 181 TPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMR 240
           TP    +L E++  + +P GV N+V+G+G +  G  + T+D I  I FTG + TG  IM 
Sbjct: 193 TPAAIMVLVELISDL-LPAGVLNIVNGYGGE-VGAALATSDRIAKIAFTGSTATGRKIME 250

Query: 241 AAATHVKPVSFELGGKNAAIIFADCDFE------KMIDGMMRAVFLHSGQVCLCAERVYV 294
           AA  ++ PV+ ELGGK+  I F D   E      K ++G +   F + G+VC C  R  +
Sbjct: 251 AATVNLIPVTLELGGKSPNIFFKDVMAEDDAFLDKAVEGFVLFAF-NQGEVCTCPSRALI 309

Query: 295 ERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVG 354
              IY  F+   + RVKA+  G P+   T +G   S E +DK+LSYF++  EEGA+VL G
Sbjct: 310 HEDIYEEFIARAIARVKAIVQGDPRKMETMVGAQASKEQKDKILSYFQIGVEEGAEVLTG 369

Query: 355 GGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKY 414
           G V    D    GF++EPTI+ G     R  +EE+FGP+  V+ F TE EA+ LANDT Y
Sbjct: 370 GKVADVSDDLKDGFYIEPTILKG-HNKMRVFQEEIFGPVVSVTTFKTEEEALELANDTMY 428

Query: 415 GLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFY 474
           GL A  W+ + N  +R    ++ G  WVN++        FGG   SGIGRE     L+ Y
Sbjct: 429 GLGAGVWSRDQNTCYRFGRGVQAGRVWVNNYHAYPAHAAFGGYKQSGIGRENHKMMLDHY 488

Query: 475 SELTNVCV 482
            +  N+ V
Sbjct: 489 QQTKNMLV 496


Lambda     K      H
   0.321    0.137    0.420 

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: 567
Number of extensions: 21
Number of successful extensions: 7
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: 490
Length of database: 506
Length adjustment: 34
Effective length of query: 456
Effective length of database: 472
Effective search space:   215232
Effective search space used:   215232
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