GapMind for catabolism of small carbon sources

 

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

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)

Query= reanno::Caulo:CCNA_01360
         (500 letters)



>FitnessBrowser__Dino:3609634
          Length = 780

 Score =  215 bits (547), Expect = 5e-60
 Identities = 151/472 (31%), Positives = 230/472 (48%), Gaps = 32/472 (6%)

Query: 8   FIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQRRA 67
           FIGG     A G+     +P  G   A+V   +  ++  A+  A+ AQ AWA    Q  A
Sbjct: 36  FIGG--TFQAPGKTFATRNPARGTELAQVTQGTEADIEAAVTAARRAQPAWARLGGQGWA 93

Query: 68  RVMFEFKRLLEVHMDELAALLSSEHGKVIADSKG-DIQRGLEVIEFACGVPHLLKGEYTQ 126
           RV++   RLL+ H    A L + ++GK I +S+  DI        +  G+  L++ E   
Sbjct: 94  RVLYAIARLLQKHSRLFAVLETLDNGKPIRESRDIDIPLAQRHFYYHAGMAALMEDELPD 153

Query: 127 GAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPVRL 186
                      R P+GV   I P+NFP ++  W   PA+A GN  +LKP+E  P   +  
Sbjct: 154 -----------RVPVGVCGQIVPWNFPLLMLAWKIAPALAMGNTVVLKPAEWTPLTALLF 202

Query: 187 AELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAAGKRVQ 246
           AE+  EAG+PPGV+N+V GD     A++ HP +  ++F GS+D+ + + +     GK + 
Sbjct: 203 AEICGEAGVPPGVVNIVTGDGATGAALVSHPGVDKIAFTGSTDVGREIRRATAGTGKALT 262

Query: 247 AMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALREKLVAA 306
              G K+  +V  DADLD AV  ++ A + + G+ C A   ++ V E  A A   KL A 
Sbjct: 263 LELGGKSPYVVFEDADLDSAVEGLVDAIWFNQGQVCCAGSRLL-VQEGIAEAFYAKLRAR 321

Query: 307 IGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQG---HEEG 363
           +  LR+G   D     G +V  AH A++           AE+V    G   Q      EG
Sbjct: 322 MATLRIGDPLDKCIDVGAMVDPAHCAKV-----------AEMVAGSNGEVHQPGTVPAEG 370

Query: 364 FFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNGDA 423
            F  PTL   ++P      DEIFGPVL      +  E + +A+  +YG    +++ N + 
Sbjct: 371 AFYPPTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYGLAATLWSENINR 430

Query: 424 AREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTR 475
           A + A ++  G+V +N       A   FGG + SGFG   + G +G+R YT+
Sbjct: 431 ALDIAPKLAAGVVWVNATNLFDAA-AGFGGVRESGFG--REGGWEGLRAYTK 479



 Score = 70.9 bits (172), Expect = 2e-16
 Identities = 56/249 (22%), Positives = 108/249 (43%), Gaps = 9/249 (3%)

Query: 8   FIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQRRA 67
           +IGG++    SG    V+ P  G +       S  ++  A+  A    A+W  T    RA
Sbjct: 511 YIGGKQARPDSGYSRPVWSPK-GVLLGHAPEGSRKDIRNAV-EAATGAASWGRTTGHLRA 568

Query: 68  RVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLKGEYTQG 127
           ++++     L    +E A  ++   G  +  ++ ++   ++ +           G     
Sbjct: 569 QILYYVAENLSARTEEFATRIAEMTGSRVPRAEAEVSAAIDRLFTYAAWADKYDGAVKPV 628

Query: 128 AGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPVRLA 187
              G+ + +M +P+GV+    P + P +  + + G A+A GN  +L PSE  P     L 
Sbjct: 629 PIRGVAL-AMPEPVGVIGAFAPDDAPLLGAVSILGAALAMGNRLVLVPSEPFPLAATDLY 687

Query: 188 ELMIEAGLPPGVLNVVHGDKDCV-EAILDHPDIKAVSFVGSSDIAQSVFQRAGAAGKRVQ 246
           +++  + +P GV+N+V G  + + + +  H  + AV     +DI+ ++   A    KR  
Sbjct: 688 QVLDTSDVPAGVVNIVTGAHEALAKPLASHLGVDAVWSFSGADISTTIEAEAAGNLKRTW 747

Query: 247 AMGGAKNHG 255
                 NHG
Sbjct: 748 V-----NHG 751


Lambda     K      H
   0.320    0.137    0.409 

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: 975
Number of extensions: 55
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 500
Length of database: 780
Length adjustment: 37
Effective length of query: 463
Effective length of database: 743
Effective search space:   344009
Effective search space used:   344009
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: 54 (25.4 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