GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Desulfovibrio vulgaris Miyazaki F

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate 8501786 DvMF_2502 glutamate-1-semialdehyde aminotransferase (RefSeq)

Query= BRENDA::B1A0U3
         (469 letters)



>FitnessBrowser__Miya:8501786
          Length = 425

 Score =  148 bits (373), Expect = 4e-40
 Identities = 107/318 (33%), Positives = 157/318 (49%), Gaps = 26/318 (8%)

Query: 52  PIVFAHAKGSSVWDPEGNKYIDFLSGYSAVNQGHCHPKILKALHDQADRLTVSSRAFYND 111
           P+  AHAKGS +   +G  ++D++  +  +  GH HP +  A+H   DR T S  A   D
Sbjct: 34  PLFVAHAKGSHLTTVDGTSFVDYVQSWGPMLLGHAHPVVASAIHAAVDRGT-SYGAPCED 92

Query: 112 RFPVFAEYLTALFGYDMVLPMNTGAEGVETALKLARKWGYEKKKIPNDEALIVSCCGCFN 171
              +    + AL G +MV  +N+G E   +AL+LAR      K        +V   GC++
Sbjct: 93  EVVLAEAVIDALPGVEMVRMVNSGTEATMSALRLARGVTGRNK--------VVKFVGCYH 144

Query: 172 GRTLGVISMSCDNEATRGFGPLMPG--------HLKVDFGDAEAIERIFKEKGDRVAAFI 223
           G     ++ +    AT    P  PG         L   + D  A+  +F   G  +AA I
Sbjct: 145 GHADAFLASAGSGVATLSI-PGTPGVPEATVRDTLLAPYNDLTAVAELFTLHGKDIAAII 203

Query: 224 LEPIQGEAGVVIPPDGYLKAVRDLCSKYNVLMIADEIQTGLARTGKMLACDWEDVRPDVV 283
           +EP+ G  G+V+P +G+L+ +RDLC+++  L+I DE+ TG  R     A    D+ PD+ 
Sbjct: 204 VEPVAGNMGLVLPMNGFLQGLRDLCTEHGALLIFDEVITGF-RVNYGGAQKRFDITPDLT 262

Query: 284 ILGKALGGGILPVSAVLADKDVMLCIKP-GQ--HGSTFGGNPLASAVAIAALEVIKE--- 337
            LGK +GGG LPV A     D+M  I P G+     T  GNPLA A  IA L  +K+   
Sbjct: 263 TLGKIIGGG-LPVGAYGGRADLMRRIAPCGEVYQAGTLSGNPLAMAAGIATLAELKKSDY 321

Query: 338 ERLTERSTKLGGELLGLL 355
           + L  R   L  EL  +L
Sbjct: 322 DALEARVAALATELQAIL 339


Lambda     K      H
   0.319    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: 394
Number of extensions: 16
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: 469
Length of database: 425
Length adjustment: 33
Effective length of query: 436
Effective length of database: 392
Effective search space:   170912
Effective search space used:   170912
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: 51 (24.3 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