GapMind for catabolism of small carbon sources

 

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

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__Dino:3607686
          Length = 506

 Score =  213 bits (541), Expect = 2e-59
 Identities = 154/485 (31%), Positives = 240/485 (49%), Gaps = 19/485 (3%)

Query: 9   NYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRR 68
           N+I G++V     +Y D V P T EV+ Q+  S+  D++ A   A  A   W K +V  R
Sbjct: 21  NFIGGKFVPPVEGRYFDNVTPITGEVVGQIARSSAADVELALDAAHAAKDAWGKTSVTER 80

Query: 69  ARILFNFQQLLSQHKEELAHLITIENGKNTKEA-LGEVGRGIENVEFAAGAPSLMMGDSL 127
           A I+      + ++ + +A   T +NGK  +E  L ++   +++  + AG      G S+
Sbjct: 81  ANIVLKIADRIEENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLRGQEG-SM 139

Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187
           + I  D  A ++  P+GVVG I P+NF +++  W    AIA GN  +LKP+E+TP     
Sbjct: 140 SEIDNDTVAYHFHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQTPAAIMV 199

Query: 188 LVELFEKAGLPKGVFNVVYGAHDVVNGILEHPE-IKAISFVGSKPVGEYVYKKGSENLKR 246
           LVEL     LP GV N+V G    V   L   + I  I+F GS   G  + +  + NL  
Sbjct: 200 LVELISDL-LPAGVLNIVNGYGGEVGAALATSDRIAKIAFTGSTATGRKIMEAATVNLIP 258

Query: 247 VQSLTGAKNHTIVLNDANLED------TVTNIVGAAFGSAGERCMACAVVTVEEGIADEF 300
           V    G K+  I   D   ED       V   V  AF + GE C   +   + E I +EF
Sbjct: 259 VTLELGGKSPNIFFKDVMAEDDAFLDKAVEGFVLFAF-NQGEVCTCPSRALIHEDIYEEF 317

Query: 301 MAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGR-ENVSD 359
           +A+   +V  I  G+       +G    ++ K + LSY + G+EEGA ++  G+  +VSD
Sbjct: 318 IARAIARVKAIVQGDPRKMETMVGAQASKEQKDKILSYFQIGVEEGAEVLTGGKVADVSD 377

Query: 360 ---DGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFT 416
              DG+++ PTI      +M ++++EIF PV+SV   K  +EA+E+AN + +  GA +++
Sbjct: 378 DLKDGFYIEPTILKG-HNKMRVFQEEIFGPVVSVTTFKTEEEALELANDTMYGLGAGVWS 436

Query: 417 SNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKV 476
            + N    F   + AG + +N    A  A   F G+K S  G    N K  +D Y + K 
Sbjct: 437 RDQNTCYRFGRGVQAGRVWVN-NYHAYPAHAAFGGYKQSGIG--RENHKMMLDHYQQTKN 493

Query: 477 VTARY 481
           +   Y
Sbjct: 494 MLVSY 498


Lambda     K      H
   0.318    0.136    0.396 

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: 582
Number of extensions: 36
Number of successful extensions: 5
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: 487
Length of database: 506
Length adjustment: 34
Effective length of query: 453
Effective length of database: 472
Effective search space:   213816
Effective search space used:   213816
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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